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"The difference was Blake and Moore, who caused our defenders more problems than our strikers caused theirs," he said after the game.
"We kept going, credit to the lads for that, but we had no cutting edge and lacked a bit of quality and pace. We had so many players missing, it was always going to be difficult, and to concede twice so quickly together made it even harder."
Looking ahead to a Turf Moor return in a fortnight he added: "We've got to forget about the cup now and get our minds set on making sure we keep well clear of the First Division's bottom three. It's not the top priority, it's the only priority."
His team mate on the field Paul Smith also shared the sentiment of preparing for league action.
"We started lively enough but lost our shape during a ten minute spell and found ourselves chasing the game," said the Gills’ captain. "I still thought we had more of the ball though but our final pass let us down.
"Still we have Patrick Agyemang at the club now and he has that pace, but we still had chances today but failed to capitalise. We didn’t really provide any firepower for the front boys and we will be working hard in training to change that.
"People mention the need for continuity and this is something we haven’t got at the moment. We need to get on with it though because we have got a good squad and the younger boys such as Matt Jarvis are now getting a chance.
"It’s a shame we are out of the FA Cup but it’s over with now and we are back to the league next week where we need to start picking up points and climbing the table.
"We need to go on a good run because we don’t want to be fighting for our lives. We could come back to Burnley in two weeks time and hopefully it will be a totally different game.
"If we do put a good run together then you never know where we could end up."
Stan was happy enough despite having to spend the second half watching for the higher vantage point of the directors’ box.
"I’m delighted to be through and in the hat," he said after the game. "The first half was scruffy until we got the goals and we were much better then. I thought they deserved it and we scored three top quality goals."
Talking about the second goal, the Robbie Blake free kick he said: "Robbie is capable of doing that but the first was a good one too and Mooro put a good ball in for the last one. That third goal was important and we got it, but the main thing in the cup is to win and as I said we are in the hat.
"From a personal point of view I’d like a winnable tie at home but from the club’s perspective a draw which would ease the purse strings would be nice.
"In the next round we could either draw one of the big boys and get some dough, be on the television and get some dough, or nothing at all and if not then I’d like a home tie we could win."
And to the half time incident with referee Graham Laws. "All I asked the referee was a civil question about why he hadn't booked Hills," he said. "I tried to speak to him at the end but he wouldn't speak to me. I don't know why. It’s a ridiculous state of affairs."