You already have a lot of great responses, so I apologize if this repeats any. :)
What about making Thomas the middle name? Samuel Thomas ___? I think it sounds like a very strong and handsome name. ;) At least this way you could tell/show them that their suggestion was used.
I had a similiar situation, only it was with my MIL. She "detested" quite a few of the names we had proposed for baby #3. More often than not, she turned her nose up to any name we mentioned that we were considering (which was difficult enough for hubby and I to agree on!). Bottom line...we named our son what WE wanted. And truth be told, it was one of the names she absolutely did NOT want her grandchild to be named. Fast forward a few months...she loves him, his name and all is forgotten.
Go with what you and your hubby want. After all, they are just kids...they'll forget all about it. If my MIL can get over it, your kids will too! :) LOL