the freeman is the messiah and the vortessence knew he would return

Kleiner was surprised though when learning Gordon had returned after Gordon was put into stasis at the end of Half-Life. But yeah I gather it was Vortigaunts that tried to keep the resistance's spirits up even if they didn't come out and directly say the Messiah was Gordon to other resistance members who only took up arms being inspired by Gordon's pushback against the HECU and later the former Xen head which freed the Vortigaunts and inspired them to help the Earth in return.

Yeah, Kleiner was in a huge surprise when he saw gordon. Also, pretty sure Eli and the Vorts knew about Freeman since the vorts could enter the g-man's void and Eli knew about the GMAN himself.

So the resistance have their intel of believing that one day Freeman might return. Unfortunately, so did Breen.

Realistically speaking Gordon would not have survived the 7 hour war; however, considering he was considered a messiah and his return was such a big deal, lots of rebels probably thought he survived all these years through fighting.