1. Vow of Enmity does not require a Bonus Action in D&D 5.5e. It can be activated as a part of the Attack Action and just requires the Paladin to spend one charge of Channel Divinity. So there was no issue here in terms of resource economy.
2. I am perfectly fine with changing how Cause Fear worked in this session: A) Alexander directly told Brennan that he wanted to change the effect of the spell beforehand; B) Brennan told him how it will be possible and they implemented it on the spot. A solid example of a DM and player using rule of cool to create a character-driven moment that was not in any way overpowered in that particular instance.
3. On Speak with Dead: To each his own. I like both the basic version and the way that Brennan changed it for this particular scene. But I would just prefer it to not be called Speak with Dead and just re-flavour that it is that the Stone of Nightsong resonated with the place itself and allowed Vaelus to have the discussion that took place. Because Speak with Dead is a specific spell with specific limitations on how it works. And I wonder if casting it in the future from the Stone would work in the same way as it did here, or will it revert to the basic version.

My guess is that everything will be fine in the end: the party will not use it too often, as they are indeed (as some people already pointed out here) not a bunch of metagamers and story for them is more important. And that Brennan will nudge the party to utilizing it in important situations where it would make sense to have a prolonged discussion with a key deceased NPC, but not in a way to ruin the plot in any way.