I think it's unlikely. But I also think authorities are sometimes corrupt. The only reason we know anything about this case is because they told us things. We're quick to believe them. Why?
I'm only suggesting that we shouldn't be so quick to take the word of the authorities. Many powerful people would be delighted to see the creators of TPB suffer punishment, justified or not. We should reserve judgement until hearing evidence.
1) Avoid tarnishing the public view of their media company where PR is very important.
2) Supporters seem conflicted ("is about other thing!").
3) The penalty of those crimes is not controversial (in this case: security information theft)
4) Therefore it doesn't cause a big media fuzz
5) Legislation about the crimes he is being charged with are not likely to change in the future so no new laws with retroactive repercussions will set him free.
6) It still inflicts fear upon similar enemies, because he's still know as "the pirate bay guy who is in jail" not the "the cracker who stole confidential data who is in jail"
It's important to realize that anytime you give the police power over people still facing trial, you give them that same power over anyone they can fabricate spurious charges against. That's why it's important to have things like warrants and pre-trial court orders, so that there's some accountability when the police detain someone over unproven allegations.
But still - it doesn't matter whether the charges are invented or not, or even what those charges are. What matters is that a judge (not the police) ruled that he should be held until his trial.