Alright for a song I'm learning a few of the bars are a C chord with strum pattern DDUUDU. I'm wondering if i can just bring my thumb and not push down on the low E, but just mute it by holding my thumb to it.
Yeah, you could do that. It's how blues guitarists play some chords.

Careful though, if it hurts, you're doing it wrong, so stop.
Current gear:
Carvin CT6M
TC Electronics Dark Matter distortion
Harley Benton 2x12, with Celestion V30s
Laney Ironheart 60w tube amp
Sure muting with the "thumb over" technique is fine really, and a great thing to learn.