It would seem that you have correctly identified the various pros and cons associated with password storage anytime you must work with a non-interactive environment. The only thought I can offer would be to possibly mitigate the exposure by having secondary accounts on the relevant websites with the minimum access you need to accomplish your goal.

At the very least, be sure than none of the passwords you must use for this are used for any thing else (but I suspect you already follow that practice.) On the plus side, It might be that these can have a high degree of randomness if you never (or rarely) enter them by hand.