Allen saw the Spireites 10-game unbeaten run unceremoniously ended at the hands of the National League table toppers.
Josh Koroma put the hosts ahead in the ninth minute with a slick finish, but the Spiterites responded well when Andrew Kiwomya headed in the equalising goal with 11 minutes to go in the first half.
Despite promising chances, Orient were able to seal another three points in the second half with goals from Marvin Ekpiteta and Macauley Bonne.
“The scoreline doesn’t tell the full story of the game in all honesty,” reflected Allen.
“We played well in patches and had good phases of play. Fenton and Shaw should have scored when it was 1-1.
“Overall it was a good performance, and for them to score off a set-play is disappointing, which is something we have been improving on for the past few months in training and in games.
“We’re disappointed, but not downcast.”
The experienced manager was left to rue a handful of missed chances as the struggling Spireites slipped to 20th.
Allen added: “When you come to these sort of places you’ve got to make chances count.
“We tried to force an error and maybe get something from our play with three up front, but we just couldn’t do it.
“I thought they started very well, they made it very difficult to cope in the opening 10 minutes, which you can probably expect coming from a team that is top of the league.
“After going 1-0 down it was a very good response from the team, they defended very well.
“I wouldn’t say we dominated the game but we were a match for them, and there wasn’t a massive gulf between the two teams.
“They had a clear threat with their two forwards, and their left-wing threat caused us problems all afternoon.
“I thought we had a really good account of ourselves when it was 1-1.
“We kept pushing and pushing, but we took the attitude well and kept going forward to attack and get something out of the game, but it wasn’t to be.”