This should still work fine since the user must click a link in order to open the window. The new code only blocks scripts that are executed automatically (through OnLoad for example).
I think these new changes are good ideas, although they are certainly going to affect the usability of some legitamite sites.
I can even see some lawsuits brewing because Microsoft could be accused of interfering with the core business of some sites - such as exit exchanges or pop-up ad sellers.
I don't think that technology is ever going to be able to solve the 'annoyance' problem of these practices. The people that use these features for malicious purposes will just find a new (and possibly more annoying) way.