The Sunnah has evidence that when Ruqya is free from Shirk, any impermissible things, and benefits then it is permissible.
Jabir reported Allah's Messenger (sallallaahu alayhi wa sallam) prohibited incantation (Ruqaa). Then the people of Amr b. Hazm came to Allah's Messenger (sallallaahu alayhi wa sallam) and said:
We know an incantation which we use for curing the sting of the scorpion but you have prohibited it. They recited (the words of incantation) before him, whereupon he said: I do not see any harm (in it), so he who amongst you is competent to do good to his brother should do that.
[Sahih Muslim Hadiith No. 2199]
al-Tahaawi said regarding the above mentioned hadiith:
In the Hadiith of Jaabir is evidence that every Ruqya which has benefit is permissible because of the saying of the Prophet (sallallaahu alayhi wa sallam):
He who is able to benefit his brother then let him do so
The Sunnah also has evidence that one can pour water on the person who is ill with the intention to treat him.
Narrated Thabit ibn Qays ibn Shammas:
The Messenger of Allah (sallallaahu alayhi wa sallam) entered upon Thabit ibn Qays. The version of Ahmad (Ibn Salih) has: When he was ill He (the Prophet) said: Remove the harm, O Lord of men, from Thabit ibn Qays ibn Shammas. He then took some dust of Bathan, and put it in a bowel, and then mixed it with water and blew in it, and poured it on him.
Abu Dawud said: Ibn al-Sarh said: Yusuf bin Muhammad is correct (and not Muhammad bin Yusuf)
[Sunan Abi Dawud Hadiith No. 3885]
Ibn Hibbaan has included the above Hadiith in his collection of Sahiih Hadiith
Ibn Baaz said it is strong and there is no harm with this hadiith
Abu Dawud was silent regarding the hadiith and he said in his letter to the people of Makkah that every hadith I am silent about is fit to be used [as evidence]
Sheikh al-Albaani considered the hadiith to be weak in chain of narrators
The above mentioned hadiith shows that you can pour water on the ill person to treat him.
وقد جاء عن عائشة رضي الله عنها وأرضاها أثر صحيح في مصنف ابن أبي شيبة أنها كانت لا ترى بأساً أن يقرأ في الماء،ثم يسقى المريض أو يصب على المريض، وأما صب الماء على التراب فلم يأت إلا من هذه الطريق التي فيها يوسف ، فيكون غير ثابت، والذي ثبت هو أثر عائشة أنها كانت ترى أن ينفث في الماء، ويشربه المريض أو يصب على المريض
And it has been narrated from Aisha (may Allaah be pleased with her) in an authentic report in the Musannaf of ibn-Abi Shaybah that she did not see any harm if one recited over water and then the ill person drank it or it was poured on the ill person.
As you can see that some scholars like Shiekh al-Albaani considered the earlier hadiith weak in chain. However, the narration of Aisha in the Musannaf of Ibn Abi Shaybah is evidence that one can recite over water and drink it, if ill, and/or pour over oneself or the ill person.
It is the part about mixing dust in the bowel of water which some have questioned.
In either case, even if the hadiith is accepted to be weak for being safe, the narration of Aisha is enough to ensure that reciting over water and then drinking it or pouring it over the ill person is permissible as she, being a Companion and wife of the Prophet (sallallaahu alayhi wa sallam) did not see any harm in doing so.
The scholars have also used this method to treat the ill person. They have made the ill person drink water upon which Qur'aanic Verses have been recited. They have also poured it onto the sick person.
قال صالح – ابن الإمام أحمد بن حنبل - : ربما اعتللت فيأخذ أبي قدحا فيه ماء فيقرأ عليه ويقول لي : اشرب منه ، واغسل وجهك ويديك .
The son of Ahmad bin Hanbal said: There were so many times that I fell ill and my father took a vessel which contained water. He recited over the water and said to me: Drink from it and wash your face and hands with it.
ونقل عبد الله بن الإمام أحمد أنه رأى أباه يعوذ في الماء ويقرأ عليه ويشربه ، ويصب على نفسه منه " انتهى من" الآداب الشرعية " ( 2 / 441 )
It has also been reported from the son of Ahmad bin Hanbal that he said that he saw his father recite ta'awwuz into the water, recite over it, and drink it and pour it on himself.
وقال ابن القيم رحمه الله تعالى
" وكنت آخذ قدحا من ماء زمزم فأقرأ عليه الفاتحة مرارا وأشربه فأجد به من النفع والقوة ما لم أعهد مثله في الدواء ، والأمر أعظم من ذلك ؛ ولكن بحسب قوة الإيمان ، وصحة اليقين ، والله المستعان " انتهى من " مدارج السالكين " ( 1 / 293 ) .
Ibn al-Qayyim (may Allaah have mercy on him) would take a vessel containing Zam Zam water and recite over it Surah al-Faatiha. Then he would drink the water. He said he found great benefit and attained strength from drinking the water. As a matter of fact, he found such great benefit which he did not find in medicines. And how much one benefits is in accordance with ones strength in faith and firmness in belief.
Thus, when it is permissible to recite into water and drink the water, then it is also permissible to recite over other drinks, foods, and permissible medications. All of this benefits and is free of any kinds of Shirk. Nor does it contain any kinds of impermissible things.
Abd Allaah bin Ibn Jibriin said:
وثبت عن السلف القراءة في ماء ونحوه ، ثم شربه أو الاغتسال به مما يخفف الألم أو يزيله ؛ لأن كلام الله تعالى شفاء كما في قوله تعالى : ( قُلْ هُوَ لِلَّذِينَ آمَنُوا هُدًى وَشِفَاءٌ ) وهكذا القراءة في زيت أو دهن أو طعام ، ثم شربه أو الادهان به أو الاغتسال به ، فإن ذلك كله استعمال لهذه القراءة المباحة التي هي كلام الله وكلام رسوله صلى الله عليه وسلم
It is proven from the Salaf that they would recite into water and the likes. Then they would drink the water and wash with the water. It would lighten pain or completely relieve it. The reason for this is because the Kalaam of Allaah is a Shifaa [cure].
Allaah says in the Qur'aan:
Say, "It is, for those who believe, a guidance and cure."
And likewise is the matter with oils and food. You can recite on them and then eat and drink them and use them to wash yourself. The reason being that doing so falls under using this permissible recitation which is the Kalaam of Allaah and the Kalaam of His Messenger (sallallaahu alayhi wa sallam).