With any buy low situation, you've got to have the cajones to wade into the depths when it looks pretty bleak.  I don't believe CJA loses his gig outright to Booker.  However, I will say I thought Waldman made a great point in his assessment of the situation regarding Elway's relationship with Kubiak and how it's been rumored in Denver that Elway has more influence over the coaching and playing time than most GMs would have.  Waldman said Elway repeatedly said that Booker was the number 2 RB on their board, so if that's the case... I'm sure Elway's infatuated with him.  And to his credit, Booker has looked good.  As for the fumbling problem, he has improved, and perhaps it's just a narrative.  NFL.com does mention it in his weaknesses on his 
draft profile page. 
Bringing it back to CJA -- Waldman speculated (in the On the Couch podcast with Sig) that Elway was stuck between a rock and a hard place with CJA.  For whatever reason, Denver hasn't ever seemed to be enamored with CJA.  They didn't negotiate with him directly this offseason - they let him go find the best deal he could find, and then they matched it, probably reluctantly.  They knew they had a Super Bowl roster, and they were going to have questions at QB, so they wanted something stable in the backfield.  That said, they still took Booker in the 3rd and, again, Elway's repeatedly said he was the number 2 RB on their board (presumably behind Zeke).  So now that Booker is flashing, maybe Elway starts pushing more and more for Booker to get more PT.  
That's cause for concern, to be sure.  However, to me that assumes a couple of things: 1) Elway doesn't like CJA, reluctantly paid him, and would prefer him to be a backup or somewhere else; 2) Elway has a strong hand in playing time decisions.  It's plausible that instead of those things, it's more like: 1) Elway and CJA's people disagreed on his value, so knowing he could match any deal, Elway let the market set CJA's price knowing full well he would match any deal; 2) Elway saw the RB position as a position of need behind CJA given Kubiak's normally run-heavy scheme and the fact that CJA's had a history of being nicked up.  Add to that how poorly Hillman played behind CJA, and how most NFL backfields have committee attacks, and the value of the pick (if your #2 RB is available in the mid-late 3rd round), and maybe that's how it all came to be?
When in doubt, follow the $$... 
CJA's new contract was a 4-year/$18MM deal.  However, it's structured in such a way that he's getting a big chunk of it this year ($6MM cap hit of the $7.6MM guaranteed).  It's *plausible* that Elway could decide to part ways with CJA after this year.  If he's designated a post-June 1 data cut, he's only $1.7MM against the cap.  That would let the team get out of his contract, BUT... CJA's salaries are $2.9MM, $4.5MM, and $4.5MM, which seem relatively cheap given the rising salary cap.
All this to say, in a dynasty, I'd still buy, though I may wait a week or two to see how it plays out.  In redraft, I'd still buy -- just more cheaply than I was looking to do earlier this week.