It's normal to have that delay after returning from a long period of sleep (hibernation). Depending on how you have your hibernate mode set up, usually it's about an hour after no use before the computer enters hibernate mode. You can note when it is by opening up your console application after you wake it from a deep sleep. Somewhere in the log it'll read something about "hibernation".
When hibernation occurs the computer won't instant on, it'll show the screen and then not allow you type anything for a few seconds. To correct this problem, you can turn hibernate mode off (search google for the terminal commands). I'm not sure if changing the settings in energy savings will do anything. I know the three settings are: display sleep, computer sleep, and put computer drives to sleep when possible. Perhaps deselecting the last option will help as well, instead of turning off hibernation.. Perhaps they are the same thing.. I have not done enough research to know that, as the 5 seconds does not bother me after a deep sleep.
Also, how'd you use safari 6 in Lion? Didn't it release with ML? So, I'm not sure how you could've had no problems with Lion and Safari 6...