Hi, is there a walkthrough for how to play the game for Caesar's legion without totally destroying most towns and wandering the Mojave Desert alone?

Destroying towns is doable in any playthrough, just dont kill towns. No town is NCR owned by definition.

You have companions for that. Raul, ED-E, Rex.

Play with the consideration of yourself as one of the Frumentarii, espionage experts made manifest. Look, dress, and operate like any other citizen of the Wasteland but whenever given the opportunity, undermine the NCR's position in the Mojave. Avoid the quests that ask you to go Rambo on encampments. Most of the interesting stuff happens later in the game and sadly requires you to not be shoot-on-sight with N.C.R.

Amuse yourself with sidequests until then. Make up your own challenges. Support factions you like (especially if they undermine the N.C.R and the Legion is in negotiation with them, like the Khans or Boomers). Followers of the Apocalypse. Work to make Freeside a hostile environ for N.C.R squatters. Explore the side quests of the Strip families.

Not sure a walkthrough exists per say but you don't need to be a sledgehammer toting psychopath that attacks NCR on sight to play Legion - you can, but a lot of the neater quests that make the faction worthwhile require spycraft which requires you to be at least neutral. After those, go on a punching spree of everyone with a military rank you can find, I left a list in another thread somewhere but I forgot what it was called. :S

Guide for playing New Vegas on the side of Caesar's Legion:
NCR = Bad
Legion = Good

That is all.

But do try to be discreet about killing NCR or use disguises cause a lot of places are under NCR rule or has NCR nearby.