If you want to know your balance you can get it from a computer that you trust. You input your public seed to "recover" your wallet. It would have to run the appropriate bitcoin software for your wallet. In addition to trusting the bitcoin software, you would have to trust the operating system, the CPU, the memory, the BIOS, most of the peripherals, etc... If you read and understood all the source code for all of this software you still wouldn't be safe. You would need to trust the compiler used to compile this source code and the compiler used to compile the compiler, etc. There is simply no way of getting around this situation. To do any kind of secure computation, you have to have a "trusted computing base".
http://en.wikipedia.org/wiki/Trusted_computing_baseFrom a practical perspective your best bet is a clean install of all of the software and then running that, reacquiring the complete block chain, etc. If you are worried about this machine being hacked, you can build an operating system that boots from DVDrom and includes all of the necessary software, starting over each time you want to check. But even then you will need to trust that your hardware (and BIOS) have not been hacked, not to mention the possibility that someone managed to get into your safe and swap the DVD ROM.
There is no limit to the amount of time one can waste worrying about these questions if computer security is one's vocation or avocation. Come to think of it, this time may not be wasted if one has a sufficient number of bitcoins. :-)