Did Kiyoshi have an injured knee even before being seriously injured by Kirisaki Daīchi High? In Kuroko no Basuke, Kiyoshi missed the first half of the year because he was undergoing rehab due to his injury against Kirisaki Daīchi High in the final match of Prelims the year before.
However, on rewatching Episode 8 of Season 2, where the flashback of the previous year's journey and Kiyoshi are focused on, I noticed that Kiyoshi looks down at his legs a number of times throughout the episode, even before the injury.
The most specific scene however is ~15mins into the episode, just after Hyuga compliments Kiyoshi on his dunk, we see Kiyoshi wincing and see his leg is quivering. This seems like a stretch that he injured his leg twice in the match.
More probable (my theory, anyway) is that he was carrying this injury before the tournament and didn't tell the others because he didn't want the team to pull out without him in the first year itself.
TL;DR - Was Kiyoshi injured before his match against Kirisaki Daīchi High or it is canon he had another injury?
After watching the episode, I think Kiyoshi started having the injury on his legs for playing too much. He may have known about it because he is tall, thus he will likely to injure his legs more than average size person (I read an article about tall basketball players are more prone to injury).

So yes, he was injured before his match against Kirisaki Daīchi High, and Makoto Hanamiya made it worse by injuring him.