Wayward Sons: Legends. I enjoyed reading that webcomic -- all of it that was online at the time -- several years ago. I just now checked, and confirmed that it's still on hiatus. Its most recent page (if you follow the link) says it will be returning "Late in 2015." Obviously, that hasn't happened.
The basic premise is just as you recall. The good guys (called "Pantheans" after their civilization, or sometimes "Ulympeans" because they were the crew of a warship called "the Ulympea") are mostly modeled on Greek gods and goddesses, with distorted names. (Occcasionally someone has a name derived from some other ancient culture, such as the Sumerian myths.)
The bad guys -- the escaped convicts, most of whom accept the leadership of "Kronos" -- are often called "Tytans" because they were all being transported on the prison ship "the Tytan." AS you said, allAll of the sentient beings involved tend to develop strange superpowers afterfind themselves crash-landing here on Earth -- where ordinary Bronze Age humans were already living. And as time goes by, the Ulympeans and Tytans who were exposed to radiation begin to manifest odd superpowers which resemble what we might expect based on the myths.
Here's a partial cast roster to illustrate how the distortion of names was achieved. See how many names you can match up with the "original" versions (which, we are supposed to assume, are actually the ones that have been distorted over the last few millennia).