The match between the third and fourth-placed teams in Sky Bet League Two ended 0-0 at Gander Green Lane, with Town failing to capitalise on the fact the home side were reduced to 10 men in the 74th-minute.
Sutton skipper Craig Eastmond saw red for a crude looking centre circle lunge on Mitch Pinnock, and although the Cobblers pressed hard in the closing stages to find what would have been a crucial winner, they were unable to do so.
With results elsewhere going their way, little damage was done to the Cobblers' league position, but top two Forest Green Rovers and Tranmere Rovers did both win to ease that little bit further clear.
And McGowan admitted he would have loved to have nabbed all three points, although a draw at a team that had won their previous five home league matches could still be a notable result.
"I think before the game we would have said it was a good point," said McGowan.
"Sutton have been flying to be fair, they are a good team and try to bully teams, and I think we stood up to that, especially defensively.
"We got a very welcome clean sheet, but with the way the game went we would probably want more out of it.
"If we go and beat Salford next week it will turn into a good point, but on the whole it is disappointing not to have won."
McGowan knew felt the Eastmond sending off should have been a key moment, and added: "You look at the clock, and you know there is probably 20 minutes left and it was a time to get round the lads and say 'let's go for it now'.
"There are times when you'd say we'll take a point here, but I think that was the sort of situation where we need to go for all three.
"I think we did that, me and Ali (Koiki) pushed on the best we could and we created good opportunities, but the ball is just not going in the net at the minute.
"But we will keep trying, we will keep working, and I am sure it will come."
On the red card for Eastmond, McGowan had some sympathy for the Sutton skipper - but not too much.
"It was one of those strange ones, so I don't know," said the Liverpudlian when asked if he felt referee John Busby had got the decision right.
"The way he (Eastmond) has gone in is bad, but I don't think he has made much contact.
"It was the way he went in though that wasn't on really, I don't think that's how you should go in with studs up and foot high.
"He wasn't going for the ball and I don't think he caught Mitch that much, but the intent was bad.
"So it is how you perceive it at the end of the day, and it meant the referee had a decision to make.
"That one went in our favour, but we have had a few that have not gone in our favour this season.
"But it was a tough one, and I'm sure it was the same for you watching. You probably think it is (a red card), and then you don't. But we just had to get on with it."