What course of action will I need to take for non-absorbable stitches causing discomfort in my perineum?

The suture that is used in a vaginoplasty should be absorbable. Some suture is absorbed more rapidly that others. Delayed absorbable suture can take 12-14 weeks to dissolve completely. I suggest you see your surgeon and discuss you what you are experiencing. After an exam you surgeon will determine how to resolve your concern.

Your first course of action is to follow up with your surgeon for an examination. It is very unlikely that a permanent suture was used in your vaginal repair. Often times delayed absorbable sutures are used which take up to 3 months to dissolve - this may be what your husband is feeling.
These sutures may be trimmed (cut shorter) so that they don't cut your husband as they slowly dissolve over time and promote healing.