The easiest way to look it is to just forget/ignore Superman 2, both versions. Look at SR as a sequel to Superman: The Movie with events occuring in between that we have never seen. Those events mainly being the romance between Superman and Lois and Lex visiting the FOS at one time. The romance between Superman and Lois is NOT what we saw in Superman 2. From Bryan Singer,
"Well, I didn't really stick to that. Y'know, the mylar bed. And the cocktails in the Fortress of Solitude. I wouldn't want to bring that up. All I wanted to reference is they had had a previous, there was some sort of previous relations between them."
link:
http://www.superherohype.com/news/featuresnews.php?id=4972
This clearly states that Singer did not follow any of the romance from Superman 2 and he did not follow any amnesia kiss. In the time between S:TM and SR, Superman and Lois slept together and some time afterwards Superman leaves for Krypton. In SR, Lois knows she slept with Superman, she has not had her memory wiped, therefore she is not flipping out when Jason pwns Brutus. Singer and Co. used the term vague history, which was a mistake IMO, b/c some of the events in between S:TM and SR were
similar to Superman 2 but they weren't exactly(as I stated above).
Singer and Co. should have just made it clear and done a better job in indicating that SR is a sequel to S:TM with some time passing in between the two films. It would have made things a whole lot easier for everyone.