the first question that comes to my head is how committed do you feel to the company you work for? I mean, do you consider yourself a part of this company or just an employee who doesn't give a shit about the company's future as long as they can afford you? Since you're discussing about filling patents based on your work, I guess you're not just the "Hi, who are you?" guy. How does the company treat you? How valuable do you feel?
You can always file the patents and then screw them after some digging in the prior ones. Is that what you really want? Do they deserve it?
On the other hand, you can just refuse to file them and get fired (probably). Can you afford that? Will you by any means miss your (previous) job?
I think that it all comes down to your professional relationship with your boss/company. There are many many ways to support the open source ideal and I think you're messing with the worst one. No one will ever see a hero in you for screwing your company or losing your job because you hate software patents. Just file the damn ones and aid the community by participating in something more valuable to it.