Assuming you started both wars, then you would have received a double diplo hit for aggression. Why did you take peace in the latter scenario?
If I'm going for a DomV and I'm besieging their capital they often offer peace, but I only take it if all of the following are true:-
a) my troops need a bit of healing
b) I will take the capital within 5 turns of starting up again
c) I have time to spare - i.e. I'm ahead of schedule as far as total capital sweep is concerned.
d) That breather won't allow them to reach their next key tech. I made a mistake once of giving a civ peace and he had musket when I restarted the assault. Not fun at that time, I promise you.
e) The monetary offer is enough to help me buy something decent in the 10 turns interlude, and/or get a WLTKD, etc.
If all are true, I'll do it. If not, I'll press on.
TLDR: It has diplomatic penalties for sure, as well as potential victory-diminishing penalties, IMO.