If I do another run through of Skyrim, but only complete the main quest line, will that then mean all of the side quests are still available to me? Meaning, will events in the main quest line mean certain npcs and their side quests become unavailable?

You'll be fine, the sidequests will all still be there for you after the main quest. I suppose there might be the odd misc. objective that becomes unavailable but I can't think of any off the top of my head

The peace conference (Season Unending) can affect a few objectives in cities that change sides. You won't have to do the Jarl favors any more to become Thane in Markarth if you take it for the Stormcloaks at the conference, for example. But no major side quests should be affected. Even Blood on the Ice worked fine for me after I conquered Windhelm for the Imperials (it started immediately after the battle). But it always does. I'm That One Guy who's never had it glitch.