Can I stop the merge process so the new SP can safely restore the latest point of the vms?
No, you cannot stop it. However, you should be able to restore from the latest restore point regardless of whether merge process is running.
Can I perhaps increase the number of copies, currently 2, to let's say 6 to keep the merge proces on-hold for a few days in the copy job
As soon as retention is reached, merge will be happening on everyday basis (assuming daily copy job is meant here). So, number of restore points does not matter here. Having said that, I still think that you'd better increase retention - two seems to be rather short value.