A router should be fine with some additonal programs.
Download Protowall and The Blocklist Manager
You could use a client that's more configurable. You can choose to use one port and use something not so common. This way, you would only have to forward one remote port in your router rather than one per torrent download.
Technically, changing clients would qualify as removing the program.
But, just in case they are using more than port monitoring, clean and tweak your system.
X-Setup <---Ultimate Tweaking tool
BlackViper's Site <---Shut down vulnerable services.
Virus and Spyware removal
You could always do a format.
They can't find anything then... unless of course your ISP is the NSA.
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