*Spoilers* Only look at this if you've done the Main Story

So my wife and I had been waiting since ESO's release to join in, but one thing after another delayed our arrival to Tamriel. Well we finally got to join the community a couple months ago and with One Tamriel were a bit overwhelmed by all the things we could do, so mostly we've just run around Tamriel gathering Skyshards and fighting group bosses.

We finally started with Quests and figured we'd do the Main Story first and last night we got to Coldharbour. What we encountered there has made us worried we've made other quests unobtainable, such as our Alliance quests. Most notably we are gathering the Restoring the Hollow City/ Army of Meridia recruits and see that some of them are major villains from Alliance story lines (such as Angof). By proceeding with this quest line and being in Coldharbour are we robbing ourselves of other quest and their rewards?

We're major immersion players and making new characters is out of the question, so we need to know if we simply need to come to terms with losing quests or not.