A throwout bearing is far from a "major" problem IMO. Depending on how you drive you may need a clutch job at some point, in which case this bearing is usually swapped out as preventative maintenance anyway. Likewise, if you are going to spend the $$ to go in for the throwout bearing you may as well do the clutch given the mileage. As for the battery, it's true that some HCH's with manual transmissions had problems with the battery if they were driven in such a way that demanded lots of assist. The CVT doesn't seem to have this problem, but then again I have heard of more '03-'05 CVTs having problems than batteries.

Does your battery show any signs of going bad? Frequent recals, etc? More importantly, what is your utilization of the battery? Does it frequently get low to the point that the car applies a charge to it while you drive or are the fluctuations in charge fairly mild? If you haven't been hard on it and it's not acting strange then there isn't a reason to believe that you will need to replace it. Not yet, anyway.

As far as making your decision goes, also do the math on a new car vs. doing the clutch and battery (worst case scenario) and driving another 100k. Odds are it will be way cheaper to do the repair and keep driving.