While I'm sure it IS possible to just replace the thunderbolt port it would be labor intensive and a specialized procedure.
So yes, this is a replace the entire logic board procedure.
Apple DOES offer a flat rate repair service for out of warranty Macs though. They talk about it a little bit in their KB article - AppleCare Direct Mail-In Repair Serivce - but I can't find a public facing article explaining the tiers and pricing.
Basically they offer a flat rate repair. Assuming your Mac is damage free (no major dents, liquid damage, etc) they will mail it to their repair depot where the issues will be addressed and parts will be replaced for a flat fee. The fee varies between models/sizes but will more than likely be less than the cost of having the logic board replaced by itself at an Apple store or AASP.
You can either arrange this by calling AppleCare (1-800-APLCARE) or visiting the Genius Bar at an Apple store or AASP. You can find nearby Apple stores and AASPs using Apple's handy locate tool, just search for Service in your area.