Well the deal with software patents is that you _can't_ check your ass.
It would require having a team of people who are experts in patent law and programming following all your developers around and checking on projects your using in order to try to link against patents.
Even then your not going to avoid lawsuits from patent trolls.
Since there is no practical defense against patents then there isn't much you can do. Sure if your notified, like in this case, then you are forced to act, but it's definitely not something you want to volunteer for, especially when your in business. No benefit for you, all pain, no profits.