"Can we still file a joint return?"
Yes, since the trust is apparently owned by the grantor (one spouse) and one other person (the other spouse), you can continue filing joint returns and treat the trust as a disregarded entity (a grantor trust). The foregoing presumes the trust instrument does not contain express language to the contrary.
See https://www.irs.gov/instructions/i1041/ch01.html#d0e1593
