Possibly, but it also helps us push to explore territory that can provide unique gameplay. With pure focus on Gameplay it can be easy to not explore more dangerous ideas or just immediately dismiss them; but often you would miss out on the insight of both what options to explore once you commit to an idea but future lessons for gods.
3/4 of your examples I would say show this pretty well works. Pushing how "disorienting" we can make his horn was a relatively low risk exercise on our part that wouldn't break the characters theme if it was not there and had some potential payoff that is could have bolstered his theme some and potentially provided unique gameplay. It was tested as a known higher risk aspect but it was a pretty easy thing to try out, iterate on, and discard if it didn't feel like an add.
Tsukuyomi's Basic Attacks is similar. It had the potential to double down on his theme and reinforce his precise and calculating demeanor and the pointedness of the ability that causes it but was not something so integral that when we removed it post launch ruined his theme.
These I would mostly say as theme reinforcements rather than themes unto themselves and for each case we might have gone too far I think we have found places where they can be real value adds. This also doesn't go over the countless times we try stuff internally before releasing it out to the world. Some things people really enjoy wouldn't exist if we didn't try some of this stuff.
Baba Yaga RNG was a gameplay hook and is one of those things I think people are either going to really enjoy or be turned away by. As long as it independently isn't so strong and frustrating as to warp enemy gameplay it can be OK for some gods to have niches as long as it isn't too extreme. It is one of a MOBAs biggest strength, you can almost always find someone you resonate with. Baba mostly saw play once we fixed other issues and bolstered other parts of her case which to me points to the RNG aspect largely hitting the mark.
Persephone would be one where yes, the theme created a negative gameplay; which we would readily admit. The idea of a character reviving to fight again is not only a very popular request but felt like a solid 1 to 1 connection and pushed it forward. We did a lot internally to mitigate how strong it could potentially be, both before launch and after launch; but it was fundamentally breaking a promise about the game in a way that was negative.
The rework version may not be as flashy but we kept it for a few reasons. The first is the passive itself does have a component that on its own is a powerful enough passive. Generating free gold is potent and we knew it was getting stronger with a faster plant generation rate. With this we figured that rather than removing entirely the ability to do something post death and bolstering the passive slightly to compensate that keeping that as some extra flavor was better. We expected this to be the most divisive point of the rework; and it was. However since then her metrics, ban rates, frustrations are all in a much healthier place (they may not be perfect but are a significant improvement from the old version) and I am unsure if changing the passive even more would have resulted in something more positive unless it was entirely (gold generation included) reworked. We were already changing a lot however and this felt like a step too far. I think this has merits to be debated from from both sides.
TL;DR While yes it may be possible that we sometimes overindex on 'theme' it does provide us an opportunity to really explore concepts and ideas we might otherwise discard out of safety and provides the team an opportunity to see what we can/can't/shouldn't do within SMITEs gameplay space. I also don't fully agree it is a scale purely between Theme <----> Gameplay; as they often intersect in a variety of ways and in a variety of extremes.