For "It('ll) all (work) out in the end", "Everything will turn out fine", how about "Tout est bien qui finit bien" ? ("A la fin, c'est pareil." would be more like "In the end, it's all the same/...it all comes down to the same thing/...it doesn't make any [real] difference.", w/out the nice/optimistic"Cheer up!" attitude.)
Hmm, A la fin, c'est pareil is the closer of the two (I am talking about something concrete...)
I'd thought of something similar to "Tout est bien qui finit bien" though that is too general and vague for this context. It's kind of like, if you would rather do it your way (after I'd asked for something else to be done) it's all the same in the end.