#1 Don't reveal your villains' names.

The spell states (emphasis mine):

When you cast this spell, you can speak the name of a specific creature (a pseudonym, title, or nickname doesn't work).

A villain who is aware of the Gate spell would not tell his name to others. Hence, your players cannot summon him, if they only know him as "evil wizard of the east" or "the hero of Parnast" (yes, that guy is a villain, no further discussion necessary).

#2 Use Contingency with Otiluke's Resilient Sphere.

You can also cast the Contingency spell on yourself, using "when someone other than me teleports me" as a trigger, and make the spell trigger an Otiluke's Resilient Sphere.

Note that this sphere can be dispelled or destroyed with Disintegrate, so it won't work if your PCs anticipate the use of this sphere.