I prefer to think of it in a little bit simpler terms: I look at it kind of like a game's characters would see a programmer... Check it out...
When I start making a game on RPG Maker, I'm in complete control of my characters, what they do, what they say, what they think, and I know everything about them. These characters, if they knew what I am capable of in regards to them, would see me as a god. I can whip them up or destroy them on a whim...and not just destroy them, but erase them to the degree that they never existed...not in their limited view of their timeline anyway. I am always the same to them, able to reach into their future or their past equally as easy as their present. It's all the same to me. What they see as a timeline, I see as a sequence of events that can be modified at any time. I can create new events that use the "teleport" command and send them to another part of the game... Which these characters may interpret or see as Gates forward or backward in time.
But what if my computer gets a virus?
Lavos is essentially this virus. Something I cannot control, nor can I readily delete it. It, too, can reach to every area of that game, corrupting or annihilating characters, areas, times, worlds.
Marle's actions caused her own demise, in terms of the time paradox. That's completely a coding thing, cause and effect. Lavos, however, as you said, was an outside force -- a virus -- that either the Entity couldn't readily destroy...or if the Entity vs Lavos is more like God vs Satan, then the Entity simply chose not to destroy Lavos immediately or directly.
Perhaps stranger yet, would be if Lavos is not a virus, but another user on the proverbial computer, trying to make its own changes. Therefore, even by negating the changes Lavos makes, the outside force is still there somewhere, in the DBT or the Tesseract or wherever.
And since Lavos has already succeeded at screwing things up to SOME degree, his after-effects will always be felt unless the "programmer" (the Entity) could halt the process, debug what needs to be fixed, and then begin from where it left off. However, because the Chrono world is essentially a running engine (time and time-error never really stop), it's more difficult to make these sort of changes.
Does that weird point of view help you at all?