Personally, I would do a separate rest with the rye malt (as opposed to flaked rye) at 110 or so for just 10-15 minutes and add that back into the main mash a bit at a time. I would think of it as a low temp cereal mash.
I run a Brew Magic and that much rye without a protease rest could stick circulation a bit and cause lautering issues. With the separate mash you can be mashing the base at normal temps and slowly add in the rye mash without dramatically shifting your temperature rests. I don't recall the mash temp to degrade protease, but if I recall, it happens quickly somewhere north of 130F. At least the circulation should help offset the temperature drop.
Best of both worlds then... and with a nice high temperature rest at mash out and the base mash not going through protease, you should avoid the potential of bad head retention.
That said - there are good arguments on either side.