One word: yes
Not only it deactivated groups are not processed, but also they help organise your project, and they also make the debugger profiler tab really useful.
If the amount of work is really too much for this project in the ned, still keep it in mind for the next project you may do.
PS: since it involves quite a lot of modifications, remember to do a manual back up before hand, so you can make mistakes without losing too much.