First of all, obviously the FA's comments that you overheard was definitely out of line, rude, and inappropriate. And you're probably justified in taking that up with customer service.
Might be a cultural thing to be honest, but I've occasionally gotten the sensation that I can't excessively dress down on planes (moreso in Japan than in the US). Several years back I landed at NRT in flip-flops, sweatpants, and a t-shirt, and even my family said, "what the hell are you wearing?" Obviously, IIRC this was in the middle of winter, so that might have had something to do with it as well.
I mean, walking in sweatpants and a t-shirt in SFO isn't really that out of place, but I certainly look out of place once I land at HND--even moreso once I head into the city. So yes, depending on where, and who you're dealing with, I'm not surprised that people saw your "pajamas" in a negative light.
When I usually dress for flights, I usually wear some khakis, a shirt and a quarter-zip sweater (around this time of year). I occasionally keep a pair of sweatpants in my carry-on in case I get unbearably uncomfortable for some reason.
Personally, I choose to maintain some baseline level of propriety while at the airport, because it's very much a public area, and not everyone's coming off a 12 hour transpacific long-haul, dragging themselves to yet another long flight. So I usually don't dress in clothes that I wouldn't commute/ride the subway in while at the terminal.
Re: the complimentary pajamas in J/F: I guess expectations change once you're in the air. Everyone's in the same boat, and people are more understanding for more casual clothing (although the increased privacy in the premium cabins might also play a role). But I think it's worth to note, at least when I was in F on JL, once I woke up, the expectations from the FAs seemed to be that I change into my original clothes (although they did fold the pajamas for me to take home).