when you have to be cruel to be kind, it simply means you are dishing out tough love to your lover. (S)he will later recognize that you have his/her best interests in mind and will later be grateful for what you are doing. Things will all pan out in the end, your lover just has to trust you.
"Cruel to be Kind" is a late 1979 hit for British rock'n'roller Nick Lowe. He's made other great witty songs as well, check out his 1989 greatest hits release "Basher: The Best of Nick Lowe", it's terrific. Also, a different song of the same title appears on the debut album "Resident Alien" by Spacehog, from 1995.