Yeah... I don't know if this post needs a spoiler warning, but better safe than sorry. Anyway, I started a new game with a Nord barbarian and I took him to Solstheim partly 'cause I had just gotten Bloodmoon and I wanted to see what it looked like. I've been there for a while, the fort's been attacked and I've done three of the stone quests that the Skaal send you on. I realize now that I should not havew gone to the Island with a such a low-level character, I want to head back to Morrowind to start up the main quest to build up stats. My question is, if I leave Solstheim, will everything be the same when I return? I don't want to screw up those quests by leaving for a long time.

You'll have no problem in leaving them at any point. But IMO if you haven't started the East Empire Company quests yet I would begin them before you leave. They have some quite long delays between quests being available. See Carnius in the Fort to start them off. Do what he asks and return to him as Falco in Raven Rock requests. Then the first wait arrives. Good time to head for somewhere else.

indeed

the first 6 (?) quests for raven rock has a 3 day delay between missions, so its worth doing your questing on morrowind until your journey tells you that a new raven rock mission is available, go there and do the quest, then return to morrowind. This way the colony develops more "real time".

youll understand once you complete it

Its worth noting however, you should complete the raven rock quests as quickly as you can, as I can tell you as a fellow low lvl char, have that smith with 10k gold is a great asset! You can hunt for weapons and buy your training so you advance really quickly