What matters most : published papers or GPA? (for scholarship and future career)
The whole package is important.  An admissions committee will be very interested in your ability to pass their coursework. It doesn't make a difference how productive you are, or how deep a thinker you are if you flunk out on grades, which would just be wasting their resources.

You would need them to believe that your MSc grades would be indicative of future performance.  

By all means, apply, and do the best to make your package look right.  Lot's of students can have mediocre undergrad grades, but figure things out as they mature.  The MSc with good grades was step 1.  Good GRE's would be important, as would letters from the profs of your most difficult coursework confirming that you breezed through it without trouble.

You might also pay attention to those programs with a big die-off at qualifiers.  If a department PLANS that 1/3 of their students will not successfully reach candidacy stage, then their grad program is built in a certain way that can deal with this efficiently.  For example, programs like this do not tend to offer much in the way of financial support until you're paired up with a mentor, and then you're in the budget of that person for support.  In a way, those programs are willing to gamble on you so long as you're willing to gamble on you.