MisterK raises some good points about granting skills and spending DPs, and then possibly taking them away. That would feel heavy handed, as a player.
That said, my thoughts after reading Druss' post were still mostly skill based. I thought of two basic scenarios. In both cases, service to the deity could result in gaining very specific skills - and I would be inclined to make those skills secondary skills, not core skills that a player will really need to develop.
The first case would be where there is really only one skill appropriate to the deity, and in return for X amount of service, the devout follower gets 1 rank in that skill.
The second case is where there may be more than one skill (nature deity, for example, might have both foraging and tracking as possible skills). The devout follower could get a small number of DP that can only go towards those skills, and then could save them up over levels if needed, but could still only spend then on the allowed skills.
If you do think you'll ever be taking away the boon from the deity, I might lean towards not using skills but using a 1st level spell as the boon. It's much more plausible that the deity can give and take small channeling bonuses, than skills that the character has spent time and their expertise developing.