The craft was used in controversial US ‘rendition’ missionsThis is apparently true, but misleading. The specific plane we're discussing was used by the CIA, but by this point had been transferred to DOJ for some time.
It's also misleading to use the word "rendition" as a shorthand for "extraordinary rendition" (which is itself newspeak for "kidnapping"). "Rendition" itself is simply the process of effectuating extradition. The term "extraordinary rendition" is doubly Orwellian, because "rendition" is the word for what a host jurisdiction does. A government cooperating in extradition renders subjects. The CIA kidnapped people, apparently without engaging any process of the host government.
To make matters worse, the CIA's kidnapping program sent terrorism subjects to foreign jurisdictions, allegedly (and almost certainly) to enable them to be interrogated by the norms of countries that weren't squeamish about coercive, torturous interrogations. The USG wanted Snowden back on US soil.
I suppose there's a coherent argument to be made that the US should have destroyed the CIA's torture charter jet, and that any further use of that particular piece of equipment is tainted by its history. To me, it's just a plane, and if we're going to do something drastic in response to the CIA's complicity (and participation) in torture, that thing should probably be a series of criminal prosecutions.
Either way, the implication that Snowden was targeted for extrajudicial kidnapping isn't supported by any evidence presented so far. So far, the facts we know about support a pretty boring narrative: the USG knew it was going to charge Snowden with crimes for which most of Europe would comply with extradition, and sent a DOJ plane to streamline that process.
It's hard to blame media outlets for reporting like this, because the story of how we came to know that this particular plane had participated in the CIA's kidnapping scheme makes for really good reading. But it's still important to know the whole story.
And this particular headline is pretty silly. Scotland is part of the United Kingdom, proprietors of GCHQ, the west's most unhinged signals intelligence agency. A DOJ plane flying over Scotland to fetch a SIGINT leaker isn't particularly newsworthy.