BoS was my very first playthrough and I was 100% on board with their agenda, and I still felt terrible during that final talk with Shaun. Couldn't even make excuses and just told him I was following orders and that I was sorry, which he rightfully scoffed at. I did the Institute playthrough immediately after and felt much better about it, though I had to limit my interactions with the BoS due to still retaining some fondness for the organization and the people within it.
The only one I felt sorry for betraying in the Railroad was Deacon.