Well, keeping the combat skills as they are has no detrimental effect on Careers. If you really want to push things away from combat then perhaps allow 6 instead of 4 points to be spent on Careers. I still think that the Combat abilities should be retained - they may not be as important in an investigative game but they still might be needed on occasion. Once the characters have been created it's up to the players how they spend their Advancement Points - that alone should skew things the direction you want. 

I'm with The Git on this one.
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Marcelo, you used the example of the X Files, but in that the 'PCs' were very combat capable. In the real world FBI agents would be trained in unarmed combat and pistol shooting, as well as other firearms skills. Agents would be required to practice their pistol skill on a regular basis. The characters in the X Files were also combat capable, so I wouldn't downgrade any PCs combat skills.

Adding extra points for Careers, or adding Boons would be the way to go (rather than loosing points from combat abilities) if you think that that is necessary.