I wouldn't worry about it. They'll have you so quiet in the mix when you record that much of that muddiness will be gone.
Seriously though, my most recent experience with this situation was when we were playing a song in drop C and one of the guitar players complained that it didn't sound tight with the bass playing this really fast low riff along with the guitars and suggested that I not match the guitars note-for-note. I told him that of course it didn't sound tight, it's not going to with everything tuned so low (IMO), which he did really have a response to.
I left that band on amicable terms due to touring commitment issues, but it did solve the problem, so yeah, maybe quit?
I should also mention that I'm a guitar player as well and I never like to play anything lower than drop D, and usually E standard will do nicely.