I remember when there were Southern only trains to London Bridge - what a joy that was, not getting on some trains, and then not getting on the connecting tube at London bridge where the gates were often shut due to overcrowding.
Then the Overground started, and it was brilliant, virtually empty, air conditioned!! and fast.
Unfortunately many other people realised this, many other people moved here because of it and now it's nice and busy! I usually get in to work for 8am so if you can do an earlier shift that is a lot better, but going in for 9 is more difficult (though always much better post Canada Water).
Dependant on where you are going, cycling or the trains to London Bridge should be an option?