The theme here is a tune to eliminate the EGR function. That really is the proper way to compensate for any negative effects related to it's deletion.
Mechanically, there are a few ways to delete it. One much keep in mind that the hot gases still will travel up to the EGR spacer. SO if your motivation is to keep the intake cooler, you really need to rip the upper and lower intake off, and block off the EGR port at the heads. The small center port only connects to one head. You should be able to easily tell which. Take a razor blade and remove the fat edge and silicone it to the head, and then install the lower intake so that the sandwiched razor blade blocks flow into the intake. There are also intake gaskets which do this (i do not know p/n) and some aftermarket heads simply don't even have the EGR ports.
There are EGR spacers designed to mount the throttle body cables to, or you could simply remove the EGR and use a block off plate.
As you can see, deleting the EGR involves a little work and $$$. It really offers no benefit either for the average street car, so waking up one day and deciding "I'm going to delete my EGR" makes no sense really. If one was assembling an engine with heads, or an intake that doesn't use the function and getting a tune anyway then it makes more sense...but on a stockish bolt-on engine...just leave it alone.