You sure can. Just turn off contact sync for that gmail account. I have 1 gmail account and 2 google apps accounts and I sync all their contacts using Soocial, then I only sync my gmail account to my droid and leave the other 2 with sync disabled. And yes, e-mail still works fine with all of them.

 

another option is create another g-mail account as primary for your droid. Then add your other account and do what was suggested above and don't let it sync. That way you could have contacts on your phone backed up without messing with all the contacts in the other account.