Knee ligament damage sustained on club duty for Leicester last weekend has sidelined Croft for another season, robbing England of their preferred choice in the number six jersey for the autumn and 6 Nations.
It has simplified the back row conundrum facing head coach Stuart Lancaster, but with Chris Robshaw, Tom Wood, Matt Kvesic and Ben Morgan pushing hard for the three slots, a difficult decision remains.
The most intriguing duel is being fought between rival England captains Robshaw and Wood, with both needing a strong start to the season to guarantee their involvement against Australia, Argentina and New Zealand in November.
While Rowntree mourns the latest setback to have struck Croft, he insists Lancaster will still be selecting from a position of strength.
"Tom Croft is a huge loss, he's desperately unlucky," England's assistant coach said at the launch of the Rugby Football Union's official ambassador for children's rugby, Ruckley.
"To come back from a broken neck, play for England and be part of a winning Lions series, only to then get injured again and miss another season....I'm gutted for him.
"I've left him alone for the time being, maybe I'll speak to him in a few more days. I've sent a text to him.
"I really feel for him because he was outstanding in the Lions series. He made a huge impact on that tour and is a special player.
"He has points of difference to his game and will be missed by England and Leicester.
"But we have a great group of players and the summer tour to Argentina saw the competition in our squad increase.
"Chris and Tom are fit and playing well. They played against each other in wet conditions for Harlequins against Northampton on Friday night.
"Chris isn't necessarily just an openside, he can play at six as well. I won't pigeon hole him into one position. And there's new blood in there as well with Matt Kvesic, so the competition in the back row is great."
The emergence of Kvesic on the summer tour to Argentina and the strong leadership evident from Wood against the Pumas have jeopardised Robshaw's captaincy and position in the back row.
The encouraging performance of the squad in South America has provided plenty of food for thought, as has the Lions' series triumph in Australia.
Rowntree, an assistant coach on the tour, insists the England's Lions contingent have benefited enormously from the experience.
"We had a camp in August in Loughborough with both of our senior squads and we sat them down and asked what have you learnt? We were actually there an hour and there were lots of findings," he said.
"Off the field they experienced how diligent the other nations are in terms of doing their homework and knowing their roles because on a Lions tour you don't have so much time to do things.
"Senior pros such as Brian O'Driscoll, Paul O'Connell and Alun Wyn Jones were very good at that. They picked up a lot of training from those guys."
Rowntree was speaking at Twickenham where Ruckley was unveiled to a group of 5-11-year olds with the ambition of making the sport easier to understand.
"Ruckley's a great idea - he's a kids' ambassador and helps them understand what we're doing. He's very friendly," Rowntree said.