Newcastle were hammered 4-0 at Parkhead, with Isak sent home to Tyneside.
The star striker had attracted an approach from Liverpool last week, though the Reds have now turned to Eintracht Frankfurt striker Hugo Ekitike.
Howe said after the defeat: "I'd say we have a few players who are irreplaceable. Your top players are so hard to find. They are so hard to recruit and develop. And make them into those players, when you have them you need to treasure them.
"We certainly as staff recognise his talent and ability. We are desperate to keep him as part of our team."
My decision
He also explained, "It was my decision. I decided to send him home due to the speculation around him.
"The last thing he wanted is to be sat in the stand watching, that wasn’t fair to him. It is difficult for me to sit here and give 100% clarity on any player. I'd never sit here and do that.
"It is football and you never know what can happen. All I can say is that Alex is happy at Newcastle, he loves the players and staff, the team.
"I have never had any issue with him other than seeing him express his talent and express himself. Certainly I am confident that he is going to be here at the start of the season."