You should not resign. The objective is to win the game, and if you have a chance to do just that you should play on, even if you're just fighting for a draw. The only thing I would consider poor etiquette is intentionally wasting time just to draw out your eventual demise.
As you mentioned there are time controls for a reason, your opponent spent more time calculating during the opening and middle part of the game, leaving them in a tough situation in the endgame. Time management is a crucial part of chess and your opponent didn't do a good enough job with that. To me resigning out of curtesy sounds like a ridiculous idea, which is illustrated by the fact that you won in the end.
Good People:
I recently played a game in which I was down a queen for a rook and a pawn. as the game entered the endgame stage. But my opponent was down to less than 50 seconds on their clock and I had more than three minutes left.
I was able to use my time to calculate my moves carefully enough to avoid defeat until their time had run out.
My question is about clock etiquette. Should I have resigned rather than play it out and win on time? Or is that what time controls are for? I only get to play online, I don't get to meet with people and talk things over with them. So I have no store of conversation and consultation with which to judge matters of etiquette and fair play.
I would appreciate any guidance that people can give me. Thank you for your help.
D. Paul La Montagne