Well, I'm not going as far as to blame the Workshop itself for this, but its current implementation just is... let's say sub-optimal, and needs fixing.
If there is such a clever failsafe, automatically putting you into a Vanilla cell when the mod-added cell you saved in gets removed, as it was the case in Oblivion with any Vanilla creatures and NPCs from in mod-added cells suddenly popping up in this one particular hotel in the IC when the cells they were in got removed, then that's actually less an issue with Skyrim, but I remember very well in Oblivion your savegame was useless, if you stored in a mod-added cell and then removed the mod.
But here's another one, more related to things I'm doing myself actually, yet still there could be other clever failsafe mechanisms in Skyrim I don't know of.
Let's say I'm creating my anthro-dragon race in Skyrim. I create one new race record, calling it DrakeDragon. This is version 1 and I'm uploading it "exclusively" to the workshop. Countless people download it from the workshop and use it in their games as their player race, make dozens of gamesaves, hundreds of hours played, with just this race, DrakeDragon.
Now I get to v2, and being me it's a "huge" upgrade. I reconsidered there only being 1variation of my race (a.k.a. listened to dozens of users crying for different versions with different textures, colors, abilities, you-name-it) and "removed" race entry DrakeDragon to replace it with a couple of DrakeDragonBlack, DrakeDragonGreen, DrakeDragonGold... etc etc... new entries with unique features.
Knowing what the Workshop will do I consider informing everybody what's going to happen, issue warnings that a major update is coming along and they should by all means unsubscribe my mod and only resubscribe once they created a clean save after switching to a Vanilla race via console... However, as you all will likely agree, I'll still not reach "everybody" in time with this warning.
The result is, those not creating said clean save before I upload my upgrade will "never" (repeat "NEVER") be able to load their savegames (ALL their savegames) again, as the race they were playing simply doesn't exist anymore and me exclusively uploading to the Workshop there's also no v1 of my plugin around anywhere for them to downgrade... now that would definitely svck, and wouldn't be surprised if the "feedback" I'll receive for pulling this trick would make me drop sharing my mods publically once and for all... and the best thing is, there was nothing I could've done to prevent this, other than "not uploading my v2 update".
Of course that's still a flawed example, considering I would never dare pulling such a trick but release v2 seperately as an entirely new subscription... yet still this would also get me some less-polite complaints for why I didn't just "update" v1, and I couldn't care less for this... but still it's only the pinnacle of things which can and will and already do go wrong with the current implementation of immediate automatic updates the Steam Workshop provides.
Now tell me there's yet another failsafe for the case your entire race vanishes from the race records, making you an Imperial with default appearance or some such,... then I'll really start believeing the game's yet more safe than all its predecessors combined ever were.