There is almost always a tradeoff between the clarity of the code and the technical requirements (speed, memory, etc.) of the program. Object-oriented languages have an overhead compared to procedural languages, but they have been shown to have many advantages over procedural languages, especially in long-term maintenance of code (bugs, etc.) and often development speed as well.
So with that in mind, I propose that MVC is worth implementing for your sake as the game programmer. Your code will better follow object-oriented principles, especially encapsulation, and you will likely have a much easier time maintaining it (fixing bugs or adding new features).
On the other hand, make sure to actually finish a game and not spend so much time working on the "engine" that it never gets done.
For more info, please read the question "Why are MVC & TDD not employed more in game architecture?""Why are MVC & TDD not employed more in game architecture?" and my really long answer.