Your actions and questions demonstrate noble concern for both your fellow man and the honor of HaShem, and it is a pleasure to analyze, on a basic level, the halachic elements you raise. This scenario, as you present it, raises troubling educational and societal issues, but we will suffice here by discussing the actual questions you have asked.
The gemara[1] states that one who pays his friend’s debt without being instructed to do so is not considered as having given his friend positive benefit; rather, he has merely removed an obstacle, i.e., the friend’s need to pay. (These legal categories are different regarding the laws of nedarim[2] and regarding whether the one who paid can demand compensation from the debtor.[3]) However, it is a given that in such a situation, the debt is considered paid, thus precluding any further demands on the debtor by the creditor. How payment by a person other than the debtor or his agent works is an important question. One possibility is a concept known as eved k’na’ani[4] – when Levi gives something to Yehuda on behalf of Naftali, it is considered as if Naftali gave it to Yehuda.[5] Another possibility is that at the time of payment, there is an implied stipulation between the payer and the creditor that the creditor receives the money on condition that he waives the debtor’s debt.[6]
Your question about kefel, which is a penalty limited to certain specific cases and does not apply broadly to all monetary affronts, assumes that in your scenario there was an actual halachic theft. However, this is apparently not the case. The coffee shop willingly gave Reuven the food, and Reuven therefore did not steal it. Rather, upon receiving the food, Reuven became obligated to pay for it, an obligation that he did not fulfill. While it is an aveira not to pay a debt,[7] such an infraction does not incur a kefel obligation.
One could argue that Reuven’s actions were considered theft because had Shimon known Reuven’s plan to “eat and run” (assuming that this was planned in advance), Shimon would not have given Reuven the food in the first place, such that Reuven receiving the food under false pretenses was effectively stealing. That is a fascinating perspective that has several related applications,[8] but we cannot do justice to this point in this forum. In any event, even if we were to accept this argument, there would still be no kefel obligation in our case. On at least technical grounds, had Shimon read Reuven’s mind at the moment Reuven would potentially have been stealing, i.e., when he received/ate the food which was already prepared for him, Shimon likely would have tried to force Reuven to take the food and pay for it, rather than take the food back.[9] Thus, at that point, his deception was not responsible for his getting the food, but rather for not paying.
In any case, one is required to pay kefel only if a special beit din makes a ruling on the matter based on two witnesses. Even if Shimon would think to go through that formal process, since we have lost the uninterrupted chain of semicha from Moshe Rabbeinu,[10] we now lack the authority to obligate penalty payments such as kefel.[11]
If we were to view the food as actually stolen, then indeed any berachot that Reuven made on it would themselves constitute aveirot.[12] However, if we are correct that the sin was not in eating the food but rather only in failing to pay for it, the food itself was permitted for Reuven to eat, and the fact that the situation was likely to lead to a future aveira (not paying) did not preclude recitation of a beracha.[13] Certainly, the food cannot become stolen retroactively, if and when Reuven ends up not paying.[14]
Whatever the aveira violated, Reuven certainly requires teshuva. There are several elements to teshuva. Reuven’s need to confess sin, have remorse, and change his future behavior[15] are obviously not accomplished by your noble actions. However, there is also a matter of practically rectifying one’s actions vis-à-vis the person whom one wronged. The Rambam[16] refers to making sure to pay any money due and also appeasing the victim for the accompanying affront. Your payment removed Reuven’s ongoing requirement to pay his debt, which helps Reuven if he would otherwise ignore his duty to pay Shimon. However, he must still appease Shimon for the upset he caused him. Perhaps you removed some of the sting from Shimon, which probably helps Reuven.
Finally, we note that we hope that your noble act did indeed succeed in lessening the chillul Hashem by showing how a religious Jew should and can ideally act.