My Inquisitor has a force rating of 4, an Intellect of 3 and the harm force ability. The power says to spend a force pip to deal damage equal to Intellect and then recive 1 Conflict. Can I spend 3 force pips to deal 12 damage?

No, the basic ability of Harm can't be activated more than once, so any pips generated after the first are useless unless you have upgrades.

If you want to do more damage with Harm, there are two ways. First, there's a Control upgrade at the bottom of the tree that adds damage equal to your ranks in Medicine, at no cost.

A bit easier to reach, however, are the Strength upgrades. For each pip spent on Strength, you add extra damage dealt equal to the number of Strength upgrades you have.

So for instance, if you have the base power and both Strength upgrades, your 3 Force points can get you 7 damage (3 base + 2 Strength + 2 Strength) on an engaged target. Strength upgrades can be activated multiple times, at least with the Harm power, so that's the primary way you'll get extra damage.