If anything, it'll probably make it more difficult for actual people trying to talk to their representatives to be heard.
Second, staff talks to each other all the time (they work in a bullpen like setting) so they are always aware of the issues that are reaching the office, especially if it happens in volumes. Interns report these calls to their managers, especially since they have to ask for instructions on how to deal with them.
Finally, any staff member worth her salt will write a memo to the principal to inform them of such campaigns.
...is a hell of a lot better than "no mention at all about that entertainment lobbyist's bill I rubber-stamped and then never heard anything about. Must not have been important."
So the congressperson isn't losing any calls they needed to take and the only person being punished is their secretary. In the worse case scenario that congressperson could have a bunch of constituents who object to SOPA and you'd be blocking those calls with your own (which the congressman couldn't care less about if you aren't in their district)
On the other hand, at the very least, it will give them a sense of the volume of those willing to do something like this in opposition to SOPA, even if they don't listen to it completely.