Leijer, a 10-year stalwart of the club, signed for Chinese club Chongqing Lifan this week.
Muscat said his departure left the club and player "with a heavy heart" but came after a frank evaluation of the circumstances.
"We decided it was best for all parties and we move on," he told Melbourne radio station SEN.
"For a number of reasons it's not good when you get a disruption … but it's not really shocking."
The deal reportedly netted Victory a transfer fee of $200,000.
A-League transfer rules allow Muscat to sign a player unattached to any club as Melbourne City did this week, bringing in Frenchman Harry Novillo to replace injured winger Damien Duff.
While Muscat may have been tempted to find a free agent for competition within the squad, he will instead be treating fit-again Frenchman Matthieu Delpierre as his replacement.
Muscat made it clear bringing in a new player would be possible but his transfer philosophy is one of quality and not quantity.
"It is easy [to get a player in] because you can get a player relatively easy," he said.
"To bring someone in at this stage, you're battling against who is available.
"If you're honest, it's someone who's not playing, someone who's not wanted, someone who's been discarded.
"I didn't think it was going to send the right message and confidence to the rest of the squad if we brought someone in."
Delpierre made a cameo in Victory's 3-2 loss to Wellington on Sunday and Muscat confirmed the Gallic giant would start against Perth Glory on Saturday night.
The 193cm defender managed just three A-League starts before suffering a foot injury in the club's FFA Cup exit to Glory in October.
It's less clear whether Brazilian star Gui Finkler will be fit to play Glory after being substituted against Wellington Phoenix.
Muscat said his substitution was planned but he was still "battling a couple of things".
"He hasn't pulled up great but he's trained the past couple of days and he's looking okay," Muscat said.