1. Unlike our universe, Sealed Realities are artificial in nature. Therefore, the realities were created for a reason by their creators, subconsciously or otherwise, as human beings simply don't do things without a reason or purpose. The same is true of any evolved organism. True randomness in actions cannot be achieved by living things.
Just because her realities are artificial doesn't mean they can't exist without the "reason" or "purpose" given to them. They're not just pocket realities made by some psychokinetic girls, you understand, they're unborn universes created by deities, and are arguably as real as the current universe everyone lives in (Even if you ignore the possibility of the universe being replaced at the end of the first book, there's still three years ago). I'm sure that the Sealed Realities could hypothetically live past their purpose the same way a car can outlive it's driver, so it speak. There does seem to be ontological inertia in the Haruhiverse, but to what extent is unknown. Either way, you're imposing metaphysical absolutes onto the story that don't necessarily exist.
2. They have basic characteristics in common.
Namely, they exist in parallel to our reality, they are based on our reality, and they can only be accessed from our reality by espers (as far as we know).
That would indicate that any changes Haruhi made are additional, and not fundamental. For instance, the time and bodily-entry issues you mentioned suit Haruhi down to the ground. Haruhi wishes to leave this universe, so regular time and complete entry into the world is necessary.
Similarly, the suspension of time and the mind-only entry of Sasaki's model suit her.
Sasaki doesn't want to create a whole new world. However, it is very possible that her Closed Spaces exist as a form of escapism for her, hence its entry condition. Such a reason for existence of these spaces would also explain why they feel, for lack of a better description, "warm and fuzzy".
My point is that they're different enough that you can't assume they have the exact same nature; they weren't made by the same designers and the two haven't really shared notes, unless the power is somehow juryrigged into behaving exactly this way, which may be the case depending on how seriously we take Koizumi's Book Two speculations, but it seems that his concern about the origin of Haruhi's apotheosis was indicating Sasaki (who may be the original source of the power and, IMHO, seems intelligent and rational enough to design the universe). Sasaki's Sealed Realities refuse to change, even when their creator is no longer divine; they seem to be so static and orderly that cause and effect might not exist for them.
Then I think the question is WHY Sasaki thinks she would lose control.
Has she lost control before? Why?
What does Sasaki really want, anyway? Kyon?
She seems to be pretty ignorant of things and just going off what her Anti-SOS Brigade told her; if she lost control before, I think she would know it, unless she's responsible for that weird alien artifact thing the Brigade dug up on Valentines!
Though I believe Sasaki wants to reject godhood because it contradicts everything she stands for: Reason, Facts, Science, Cause and Effect. The power everyone wants to give her makes rubbish of all that. Espers she can understand, Time Travel she can explain, aliens she can accept. But the power to rewrite the universe in ways that the laws of the cosmos shouldn't allow? That would be like Haruhi learning from John Smith that there's nothing special in the universe.
Also, more crackish theorizing: Both Haruhi and Sasaki say the same thing about love, but Sasaki admits that she heard it from someone else. Who could this person be? Haruhi herself? A time traveling Kyon? (That last really would make everything Kyon's fault.)
A time traveling Kyon is what I suspect, as Haruhi and Sasaki don't seem to recognize each other, though it would be pretty interesting if Sasaki learned it from Haruhi in some weird, subconscious manner, such as, like, I don't know, Haruhi's only loaning Sasaki's power, and while she has it, all her subconscious thoughts are an open book to Sasaki?
Even more crackish theorizing: Maybe the reason everything female seems attracted to Kyon is because the world's former (or current) god made it that way?
And so Kyon is God.
Even more even more crackish theorizing: Maybe this entire series is just a god-powered Sasaki granting Kyon's wish to see a world composed of the fantastic.
Maybe the huge twist is that Sasaki and Haruhi are both halves of the same God, and Haruhi stole Sasaki's half and causing a cosmic inbalance!
And the unified form of both girls and thus the true form of God is Tsuruya. F*cking Time Travel.