While I agree that it shouldn't have been as easy as it was, I don't think I agree with Jon never confronting his mom at all and just leaving behind a letter. That's a REALLY douchey thing to do to your own mother. Especially after everything she's already been through with him. Them talking it out like this was the best way to do things. It just...probably shouldn't have been as carefree of a conversation as it ended up being.
Of course one could argue that, with this being time travel, Lois may very well not even notice when Jon leaves. He could go to the future, come back like two seconds later, and be like "Hey Mom. I was gone for like..a whole month". But then that assumes he makes it back at all. Anything can and did happen in space. Same could be said for the future.
I liked the interaction. I'd even go as far as to say I loved it....but I also think it should have been more. Guess that's a testament to how well Rucka writes these two (awkward "Pa" stuff aside. Seriously. Did any of these people read the previous run?). Even when the interactions are lacking, they're still really good XD