Yes, that is exactly the reason. WotC designers balance their PrCs with class requirements in mind, but it's considered unseemly to say that so they couch the class requirements as "X levels of sense motive" or "Y levels of intimidate" or even "proficiency with all martial weapons". If your character can get ranks in a particular skill faster than he "should" be able to, then you may be able to enter a PrC earlier than WotC planned, which is potentially unbalancing with some PrCs.
PGtF has a regional feat that grants proficiency with all martial weapons. That poses a problem for classes such as the eldritch knight that require 1 level without casting advancement but couch the requirement as "proficiency with all martial weapons." In that particular case, WotC decided it's OK for a regional feat to do this since regional feats are supposed to be more powerful than normal feats. By the same logic, you could probably create a regional feat that would let 1 or 2 skills become class skills for you.
If you want to stay strictly within the limits of published Wizards material, your only real option is to find a class that has intimidate and sense motive as class skills, level up in it once, then spend the rest of your career paying cross-class prices to bump them up. At least then your maximum ranks will be as high as possible.
(With there being so many official prestige classes now for clerics, perhaps you could even find one that has intimidate and sense motive as class skills and also has full spellcasting progression. If so, you might be able to accomplish your objectives without sacrificing any casting ability.)
