It seems like a great game, its just really hard. Is the ending worth going through miles of backtracking?

Every Half-Life game that I've ever played has been worth the effort of playing. They all have great storylines and gameplay generally, and they're just fun to play.

I'd have to say yes, seeing as how I own every half-life game and purchased the Orange Box.
Hell yes
do it
it's definitely worth it if the game is good, which it is.