MMM can be resource intensive, I'm trying it again with my mod load on a quad core and notice slowdowns, and works best if I reboot fresh and don't have the GECK open, a browser with 42 tabs etc (wyre flash was svcking .5 gig memory, HOLY COW) but I've removed other mods such as S Storms and EVE and don't have FWE, and so far it is not too bad.
To remove mods other than ussing FOMM you could try Wyre Flash (bash) whatever, or just go directly to the fallout data folder and move anything Marts Mutant Mod xxxx to another folder or even the trash