Prevent Safari from opening minimized window
One way is to use built-in way to open new window while clicking on link. ⌘ + , to open Safari preferences &gt; Tabs and one can see following options:

So ⌘ + ⌥ + click will open link in new window and makes it active. By adding ⇧ will not make new window active.
Also - what action you call minimizing? Because I can't reproduce any sudden window opening if window is minimized (⌘ + M)