I doubt very much Jones could stop Fedor from taking him down. He ragdolled Semmy Shilt who was 260 lbs and even lankier than Jones as he were nothing. And, on the ground, Jones would face the most vicious ground-and-pound ever that makes Jones' elbows seem like nothing in comparison.
Make no mistake about it: Fedor in his prime was no joke: hardest puncher ever in MMA, most versatile takedown artist ever seen in any weight class, and an absolute finisher on the ground with vicious GNP and basic but good submissions. AND he was a heavyweight.
Jones wouldn't be able to stop Fedor from taking him down, and even if he could, he wouldn't be able to beat Fedor in a standup war due to Fedor's explosiveness and the constant threat of the takedown. Jones's low kicks are extremely risky against a Judo/sambo master like Fedor, and using them would result in Jones being taken down. Without them, Fedor would just move forward the whole time until he caught Jones or win by points.
Jon Jones would not stand a snow ball's chance in hell against a prime Fedor. Fedor was stronger, more powerful, had more versatile takedowns and a more proven submission game.
Fedor in his prime was an absolutely ungodly fighter. Jack Slack, who is extremely critical of even the most elite fighters, has stated that Fedor was the closest thing to a "flawless" fighter, blending striking with takedowns better than anyone, and the best overall ground game, mixing striking with submissions on the gorund like no other.