I think the Dark Apostle is fine as a Chaos Lord - they are, after all, essentially the Word Bearers equivalent, for all intents and purposes. The Daemon Prince's +1 to combat res isn't the reason for his cost, it's just a cherry on top. Static combat bonuses are very rare in 40k, and there are good reasons for that... but in and of itself it's not a giant bonus. Removing it would make me feel better about it's cost, but not enough for me to feel comfortable with a discount.
As for the Daemon Weapon, I'd be tempted to scrap the special rules, drop the upgrade cost by 10 points, and just give them the Chaos Undivided version of a Daemon Weapon from the CSM Book. Now that I think about it the Warp Focus ability would grant Warptime or Wind of Chaos for free - in addition to the normal Daemon Weapon bonus.
As for fluff, I'm reasonably certain Chaplains didn't exist before the Heresy, with the exception of the Word Bearers - they certainly wouldn't be using the consecrated wargear that Chaplains use. No Imperial Church to make it, after all. Chaos is certainly capable of corrupting Imperial Artifacts, but since Chaplains almost always die when a Chapter goes Renegade, and these are Word Bearers anyway.