OK, so we are developing an network related application where the user can upload their own python scripts to decide for an algorithm. Our code contains c and cython and python modules. 
Since avoiding latency, memory footprint and minimal processing is critical for us, we were wondering if it's a wise and effective (performance wise) to turn off garbage collection and handle memory deallocation ourselves.
Just develop the application so that it is functionally correct. Once you've got a correct application fire up the profiler and determine where the slow bits are. If you're worried about user script performance, you're probably focussing on the wrong thing.
A shorter answer is that it is probably unwise and ineffective to try to optimize before initial development is complete.
Does garbage collection make python slower?