Ultimately, the best evidence I can come up with is an editorial writer for The Daily Beast claims to have spoken to an un-named former senior White House official that claimed that former Secretary Acosta was asked about the light sentence he offered Epstein by the Trump Transition Team and made the claim that he was told by higher ups to drop the case as Epstein belonged to intelligence.
The claim appears to have originated in a 9 July 2019 opinion piece by Vicky Ward on The Daily Beast.
A couple of years ago, I was interviewing a former senior White House official when the name Jeffrey Epstein came up.
Unaware of my personal history with Epstein, this person assured me that the New York financier was no serious harm to anyone. He was a good guy. A charming guy. Useful, too. He knew a lot of rich Arabs, including the crown prince of Saudi Arabia, and, further, he had clever ideas about creating bond issues for them. “OK, so he has a girl problem,” this person threw on, almost as an afterthought.
Epstein’s name, I was told, had been raised by the Trump transition team when Alexander Acosta, the former U.S. attorney in Miami who’d infamously cut Epstein a non-prosecution plea deal back in 2007, was being interviewed for the job of labor secretary. The plea deal put a hard stop to a separate federal investigation of alleged sex crimes with minors and trafficking.
“Is the Epstein case going to cause a problem [for confirmation hearings]?” Acosta had been asked. Acosta had explained, breezily, apparently, that back in the day he’d had just one meeting on the Epstein case. He’d cut the non-prosecution deal with one of Epstein’s attorneys because he had “been told” to back off, that Epstein was above his pay grade. “I was told Epstein ‘belonged to intelligence’ and to leave it alone,” he told his interviewers in the Trump transition, who evidently thought that was a sufficient answer and went ahead and hired Acosta. (The Labor Department had no comment when asked about this.)
All other mentions of this seem to eventually end up with this article as it's sourcce.
It does not appear that Secretary Acosta ever made the claim himself. Wikipedia says
Acosta later said he offered a lenient plea deal because he was told that Epstein "belonged to intelligence", was "above his pay grade" and to "leave it alone".
However, two of the three sources linked to this part of the article are the Daily Beast and Observer articles listed above, and the third is from Vox but only claims that the un-named official from the Daily Beast article said that Acosta said it.
As you can see, the evidence for this claim is flimsy at best. As John Marshal of Talking Points Memo states in the article above
It’s quite hard to know what to make of this claim. As one of my colleagues just pointed out to me the dialog itself seems more out of Hollywood that something you’d hear from a former US Attorney. On it’s face this sounds like second or third hand information, which puts some question over its reliability and may explain the movie script dialog. More importantly, Acosta is hardly a reliable fact witness in this case. He has every reason to deflect responsibility for the deal he made with Epstein. Finally, it seems highly improbable that Epstein “belonged to intelligence”.
Overall, it's not surprising that Conservapedia did not cite their source in the article. Conservapedia is, by it's very name, a conservative information source, and is rated "Extreme Right" by Media Bias Fact Check, whereas the original source is from The Daily Beast, which is rated "Left" by Media Bias Fact Check. Conservapedia's own article on the Daily Beast is extremely critical of the website, and it is unlikely that the writers of Conservapedia would cite a liberal news source as their source of the claims.
Furthermore, Conservapedia is a strong proponent of President Donald Trump, yet the article on Jeffery Epstein makes no mention of the fact that the supposed claim originates from an interview with the President's eventual first Labor Secretary. Conservapedia's article on Secretary Acosta is extremely light, and makes no mention of the either the supposed Epstein connection made in the Daily Beast, nor in the actual Epstein connection that led to his resignation on 19 July 2019.