As with any lithium based battery, overcharging causes individual cell instability. You will greatly effect the performance of the pack if its overcharged just as much as you will if it is overDIScharged.
Some information can be found by googling lithium battery charging/discharging procedures, but here's a link to the wikipedia page that explains specifically lithium ion/polymer batts, such is the type in our specific case. Honestly, I doubt very much you will do any harm from using the dock, whilst having the battery in, but as with most batteries, they don't like when you just keep giving 'em juice over and over and never really discharging them. Also, try using the dock without plugging in the cord. Just some thoughts, as I've ruined my fair share of lithiums in my RC heli's and planes. Don't be afraid of just taking the battery out either. Remember, that's a feature we have over every other tab on the market. The Thrive will function without a battery installed, FYI.
So, oorah to USER REPLACEABLE BATTERIES!!!!!!!!!!!!!!!!
Cheers and Good Luck
Edit forgot the link:
Lithium-ion polymer battery - Wikipedia, the free encyclopedia