I agree with the treatment approach thus far.
Surgery, cryotherapy, imiquimod, interferon, 5-FU gel
are all options to treat condylomata acuminata. Normally, the imiquimod is not indicated for internal use.
If this option fails, you can discuss the other approaches. A referral to another urologist - preferably at a major academic medical center - or an infections disease specialist can be helpful.
Until treated, I would suggest barrier contraception to reduce the risk of transmission.