Charging cool batteries is better than charging hot batteries- I hate to be so nebulous, and certainly I would think there are some temperature cut-off features in the on-board charger to prevent charging the batteries > ~45 deg C (~120F). However, that's still pretty freakin' hot.
It's also probably "better" not to recharge your bike immediately after riding it- the batteries get hot discharging as well as charging, so if you wait a while and let them cool down, that might help, as they will disipate heat again during the charge phase.
As far as I know, ALL electro-chemical processes (like charging/discharging batteries) are severely temperature dependant. I believe that Brammo/Valence has likely done some good homework and designed a battery management system to mitigate problems with charging over temperature.
Having said all that, it's also probably better to utilize these features as little as possible. The less abuse the batteries see, the longer they will last. Period. Same goes for just about any machine- the more you abuse it, the shorter it's useful life.
Usually battery cycling capacity is measured/calculated using rather ideal lab conditions, including discharge characteristics, charge characteristics, and temperature.
I would bet that the 1700 charge/discharge cycles that the batteries within the Brammo are rated for would be a substantially lower number if this rating was done at elevated temperature- I could very well be wrong here, since I don't have a data sheet for the battery in question.