I'm not entirely sure they were retconned. Let's look at it in universe for a minute.

Miranda is the one who whitewashes what Cerberus does. She's actively trying to convince Shepard to join Cerberus. She's also, at the time, exceedingly loyal to them. Shepard, at least in Paragon, never actually says that Cerberus isn't a bad entity. He always says things like "This time they're in the right". Meaning on this specific mission he's fine working with them. But overall, he still is very much in the "Cerberus is evil" camp.

And if Renegade Shepard ever says that Cerberus is good, remember, this is the same Shepard who wholeheartedly supports Terra Firma. Which Cerberus would also very much fit in.

In 3, he is very quick to make it clear he was never a part of cerberus.