Is it proper to say "Welcome back" after someone visits Israel because of the lower level of Kedussah between Israel and Chutz LaEretz?
Yes Yes Yes Yes Yes, you should always welcome people and be nice to them.
Why would it be any different than someone leaving Shul and going onto the subway?
I can't see the problem with saying "welcome back".
What might be considered innapropriate is "welcome home".
Jews should always consider their country to be Israel. Devarim Rabbah records a conversation between Moshe and Hashem, where Moshe complains that Yosef's bones will be buried in the land of Israel, wheras he, Moshe, will be buried outside of it. Hashem responds that Yosef identified himself as from the land of the Hebrews, wheras Moshe didn't correct Yitro's daughters when they described him as an Egyption. Moshe was reprimanded for this even though he had never even set foot in EY.