Is it permissible to fulfill a vow of praying two rak'ahs for every cigarette a smoker smokes if he returns to smoking, knowing that the basis of acts of worship is built upon prohibition?

This vow falls into one of three categories: 1. A vow of obstinacy and anger, in which case you have the choice between fulfilling it or offering an expiation for an oath. 2. It is not in the form of a vow or anything that indicates it. 3. A mere thought, without verbalization, which carries no consequence.

Smoking is forbidden, and you must quit it; the vow further emphasizes this.

As for your statement that the origin of acts of worship is based on prohibition, if you mean that they are not obligatory unless there is evidence from the Law, in objection to their obligation in the case of a vow, then the answer is that a vow becomes obligatory to fulfill because the one who made the vow has bound himself to it.