I know people who shove their CD trays on their PCs back in after placing the disk on top. IMO that's WAY more destructive. If you lightly tap a CD tray it goes back in on its own, but I usually press the button because I care about my technology and want it to last. As for what you did, I don't think it's a huge issue at all. The motor went on my old big PS2 tray, which is why I preferred the slim pop-top model. But the PS3 newer version of cd eject has always worked well for me no matter if a game was on or not. The only thing I would check is where your game was last saved.
One thing I miss is playstation 1 (not sure if 2 had this) you could eject a game once a level was loaded and play a music cd in the background. Used to do this all the time.