Holden sustained cruciate ligament damage in a tackle with Jonny Evans in the 1-0 defeat by Manchester United two weeks ago for which the defender received a red card.
Holden is expected to be out for around six months, meaning he will miss not only Bolton's FA Cup semi-final trip to Wembley next month and the end of this season but also the start of their next campaign.
Coyle said: "Let's hope it's sooner than that but what we have to make sure is it's the right time and we're not rushing people back in, because it would be detrimental to everything we're trying to do."
It is Holden's second serious injury blow in 12 months after he suffered a broken leg on international duty last term, recovering just in time for the World Cup finals.
The 25-year-old has been one of Bolton's best players this season but Coyle believes his previous experiences will stand him in good stead as he begins his recovery.
"Stuart is obviously disappointed by what has happened to him, and what happened to him last year when he had a broken leg," he said. "He managed to bounce back at the very end of the season to go to the World Cup so he knows how difficult it can be when you're injured.
"But he has such a positive mindset and we encourage him in that to make sure, when he comes back, he comes back bigger and better. He did that the last time and he will again.
"He's set for a glittering career, so, as disappointing as it is for him now, as I said to him, he's got to look at the bigger picture and know he's got so much to look forward to."
With Mark Davies still battling an ankle injury, Coyle is short of resources in central midfield for Saturday's trip to Birmingham, but he has backed the likes of Fabrice Muamba and Tamir Cohen to seize their opportunity.
He added: "We've shown before when we've picked up serious injuries that the lads can cope with it, and what it does is allows somebody to step into the fray and show their quality."
Coyle had better news this week in the shape of Gary Cahill, who shone on his first senior start for England in Tuesday's 1-1 draw with Ghana, and his manager is sure it will not be his last.
"People have said he looked like a top player, that's because he is a top player," Coyle said. "The great thing I think for England, with the way they're looking to play, it looks like Jack Wilshere will be pivotal and those type of players in midfield, the Lampards and Gerrards, what they need is players at the back to pass the ball out to them, and there will be none better at that than Gary Cahill, because he's so comfortable on the ball."
Coyle has consistently said he would not stand in Cahill's way of a move to a bigger club, and he has no reservations about the increased exposure the defender is now receiving.
He added: "Any clubs that come calling for any of my players, it will be on the back of how well they have done for Bolton Wanderers, so that's not necessarily a bad thing. If and when it comes about, we'll deal with it as a club."
Meanwhile, Bolton's 23-year-old goalkeeper Adam Bogdan has signed a new contract to keep him at the Reebok Stadium until the summer of 2014.
Coyle said: "Since I came to the football club he's been outstanding and to have a young goalkeeper of that ilk commit himself is great news for everybody."