If I have a key rune activated and then I use galvony township, the key rune will get a counter. My question is will the 1-1 counter stay on the key rune when it stops being a creature at EoT?
Yup all counters stay unless otherwise stated, they just won't give any bonuses while the permanent is not the proper type to recieve the boost.
RESOLVED
I also say yes science it it a counter and not one that says until end of turn also to add you can only get the counter on it if it is morphed.
All counters stay on permanents unless otherwise stated, or a change of zones occurs. You would keep the +1/+1 counter(s) on the keyrune. Just adding more confirmation.
A counter will indeed stay on, as counters don't care what type of permanent they are currently on.
Auras will fall off however, as they say "enchant creature" and when the card stops being a creature, it's no longer valid and falls off. An aura that says "enchant permanent" would stay, though.