Kabongo Tshimanga’s 11th goal of the season was enough to secure a fourth straight victory and close the gap on leaders Grimsby Town to one point.
Tshimanga finished from close-range in the first-half but Town lost skipper Gunning after he took a boot to the head early on.
"He is in hospital at the moment with a broken nose and a laceration to his face,” Rowe said.
"You know it is not a good one because it has to be pretty bad for him to come off. Where’s the protection? I don’t want to get anyone booked but the law is the law.
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"It was a disgraceful tackle on Curtis Weston at Southend – nothing, a kneecap breaking tackle at Wrexham – not even a foul, and then here tonight.
"I am concerned about the safety of my players going onto the pitch at the moment. There are too many things going on. There was another one in the second-half where Jamie Grimes has nearly got kicked in the head as well.”
Danny Rowe missed out due to illness but there was a surprise return on the bench for Saidou Khan who came back ahead of schedule.
Jim Kellermann went off in the second-half with a tight hamstring.
Rowe acknowledged it was not the prettiest of games but was glad to take the three points which keeps them second in the table.
“It was scrappy as hell but I will take it all day long,” he said.
"For all the plaudits on Saturday we got for the way we played, this was a different type of performance.
"We dug deep and we showed passion and we played for the badge and that is the minimum requirement.
"We have got to pick up as many points as we can in this first-half of the season and then come the Christmas period we will start getting some bodies back and get back to full strength.
"We are suffering, I had one sub left and I had to wait because Saidou has only just come back from injury and he only had 20 minutes in and he played 25 and he ran his heart out.
"I could not change our shape to combat their shape until that moment.
"Once we did that (change shape) we regained the game and we were not really in any danger, we should hurt them more on the counter-attack and switches of turnover but we weren’t quite ruthless enough.”
He added: "Despite their possession in the second-half we restricted them and they did not really test Scott Loach.
"It was a solid second-half performance but we know we can do a lot better with the ball.
"In the first-half I thought we were a bit wasteful when we got into attacking positions, the final delivery was not right.
"Thankfully Stefan Payne was very unselfish for the goal and Kabongo was there to get his 11th goal of the season.”