For a while the weather threatened to intervene when the game was halted for 27 minutes in the first half after the pitch became waterlogged following a torrential rainstorm.
It came just after Scunthorpe had recovered from a nightmare start, with Luke Norris firing Gillingham into a second-minute lead.
But Iron teenager Hakeeb Adelukan equalised with a stunning shot in the 11th minute and eight minutes later Gary McSheffrey produced an excellent finish for his second goal in successive games.
“The referee was right to bring the players off when he did in the first half,” said Kelly.
“But I don’t think there was ever a danger of the game not finishing.
“The referee said he wanted to give it 10 minutes or so to see if conditions could improve. But everyone was keen to get back on.
“I thought we had played really well until it started raining. Obviously it was disappointing to concede a goal so early in the game, but we have some big characters in this squad.
“I don’t think their goalkeeper saw the goal that Hakeeb (Adelukan) fired past him.
“And the second goal from Gary McSheffrey was well taken. It was a good team goal.
“We had to go a bit more direct when play restarted because the ball was sticking.
“And we created three or four chances to have won the game more easily.
“But we have got to be pleased with the result and we are all just delighted to be safe.
“Now the hard work begins this summer looking to rebuild the squad to try and take a step up next season.”
Gillingham boss Justin Edinburgh could not fault his players as they finished their away programme this season with a 10th defeat.
“We started very well with that early goal from Luke, but were then the instigators of our own downfall,” Edinburgh said.
“We were guilty of giving away the ball when we had good possession and each time it ended up in the back of our net.
“They were individual errors, but my players are good young pros and I am sure they will learn from those mistakes.
“After the rain came, I thought the game fizzled out a bit. We had a lot of pressure in the second half without really creating too many chances.
“But it was quite a bizarre first half. When the referee stopped the game, we conducted ourselves properly and took the players back to the dressing room to wait for a decision.
“I can’t fault my players’ attitude. We wanted the game to be finished.
“In fact I think both teams played to an excellent standard in difficult conditions.”