They don't have that covered in canon, and it is possible to cover it out of universe. Likely, you are right. It could be destroyed - or blasted into space (or into the Sun), or it could lead to a future situation. That's all in-universe. (Also, if you're looking for a way to fill the plot hole, we'd have to do it "in universe" with what is in that universe.)
Out of Universe
I'm not going to cover out-of-universe because that's easy and lets us just blame the writers (which is really not fair, it's like the out of shape guy who never played football thinking he can tell a star quarterback what he should have done). So I'll stick with the in-universe situation. (But from out of universe, I think there's no doubt you're right and it's either a plot hole or something left for future development.)
One more out of universe note: One of the executive producers is Brannon Braga, who loved to play around with time travel and strange results in Star Trek: The Next Generation, so the idea of it creating a paradox is possible.
The first issue is how those in the 2140s knew where and when the wormhole went. Let's make it easy and say they somehow knew it was 85 million years ago. That's a long time for anything to survive and they want it to be detected after civilization develops technology, not before. Which brings up the question of what they could possibly put in a probe that would last 85 million years.
The only answer, at least in 2012, is radioactive materials. Also, there's a need to make sure that whatever they develop would survive, even if it ended up in a volcano. (However the Carnotaurus was in what is now Argentina, and with that knowledge, they might not have felt vulcanism was a threat.)
Rather than use just one substance, they could take several different radioactive substances and combine them into a nuget that would make the radiation look like just background noise unless someone knew what they were looking for (and nobody would know that until after the probe was made, so it wouldn't change history). (Also, it's stated the probe was sent with a beacon, which means radioactive material is still a possibility.)
Once that's done, the next step is to embed the radioactive material in something that will withstand lava flows and intense pressure. Not something easy to do, but it's possible, especially allowing another 130 years or so for them to develop the technology. Once that's done, send it back. Even if they try to destroy it, it was intended to withstand a volcano, so it'd be pretty rugged.
Also, LucasTaylor has been working on the math around the wormhole, so it's quite possible that he proved, after the fact, that it's a separate time stream.
But if it were the same time stream, then after they sent the probe and the first few waves of settlers through the wormhole, any effect they'd have on the 2140s would have already started to show.
So the likelihood of it being in the same time stream is rather slim, all things considered. Especially since, after Terra Nova was established, and knowing it was somewhere in Argentine (where the Carnotaurus was), they could use imaging techniques and other technology to find any traces of a civilization or plastic materials that might have been left over from the colony.