Modifying or disabling the EGR system will void your 5 yr/100K mile warranty in a heartbeat. Have to assess the risk vs. reward and I think you'd be better keeping the warranty intact. I've used my warranty three times in three years (none of it EGR related) so its definitely worth keeping to me.
In reading dieselstop.com, there are three ways people get around the EGR issue:
1. Disconnect the electrical connector. It defaults to the EGR valve to the closed position but will cause the computer to throw a code and the check engine light (CEL) will come on. The engine supposedly runs just like before.
2. Buy an upgraded EGR cooler like this
http://www.ntshoptools.com/Ford_Power_Stroke_EGR.html or a bypass/delete pipe that removes it altogether. If this ever happens to me, I'll spring for the upgraded part rather than pay for more headaches down the road by staying OEM.
3. Most tuners disable the EGR cooler in the computer in such a fashion that it doesn't throw a code or the CEL. This is a neat feature and if the engine wasn't prone to stretching headbolts, I'd seriously consider one. Maybe with the Badger heat management vents, a mild tune, and mature use of the right pedal, the engine could survive unscathed.
As others have stated, the best advice appears to be install a coolant filter. I want to do that on ours and am looking at doing it off of my rear heater lines so I don't have to mess with the crowded conditions in the engine compartment.