I’m sorry it’s been frustrating to you. I assure you that the goal is to improve the community for everybody, and I’m fairly sure I can convince you it accomplishes that. 
In general when things branch too far off topic, it makes sense to create a new topic. Or, when things get posted on the wrong topic, it makes sense to move them to the correct topic.
The goal is to improve conversations by focussing them, but without squelching the ability to have side conversations that are beneficial. This makes the whole experience better and easier for new people to engage in a conversation without having to sort out multiple conversations taking place on the same page between multiple multiple groups of people (often with overlap, to make things even more confusing). These decisions are obviously a bit of a balancing act in multiple ways. For example, in spite of the potential for confusion when a topic is split, it overall makes the community much easier for people to participate in because it drastically reduces confusion overall.
Things are almost never deleted, though authors have the ability to withdraw posts. Even then, there is typically a visible notice left in place for a time to reduce confusion. We have taken the opportunity to convert some things posts to private messages between the moderators and commenters, when we felt it appropriate. This would appear to be deletion, but again a notice is inserted.
Some examples of how this works will probably help:
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This post, which has nothing to do with the topic it was posted in, has been split to a new topic and put into the appropriate category: “Helpdesk”. Other people will now be able to find this topic and read the answer without stumbling upon it unexpectedly and unhelpfully in the middle of a conversation about sexuality.
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In the case you are asking about, the discussion at Being a biblical woman outside the church and home was focussed on answering the following question:
“Assuming those we are teaching have good will and a desire to learn, how do we apply biblical sexuality beyond the church and home to women?”
One person basically questioned whether we should attempt do do so in the first place, which was a completely different conversation, and really had the potential to sidetrack the conversation and prevent the original question from being answered. So I split his question out into a separate topic called Should sexuality affect our work outside the home and church?
If you scroll through the original topic, you will see the following notification inserted into the conversation:
After 7 posts that only answered this alternate question and ignored the main question, it was clear that it was a separate conversation. So I split it out. This succeeded in confusing you, apparently, but it also succeeded in allowing both conversations to continue without distracting from each other or allowing one of them to suck all the oxygen out of the room.
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Then this morning, Ken posted on the second topic. Unfortunately, it really should have been on the first topic, (which is why you assumed that was where it was when you answered him). Thus you were confused when you later went to the first topic and found both comments missing, and assumed they had been deleted. So what had happened is you had both accidentally just commented in the wrong location. Thankfully I can fix that. So after you couldn’t find them and asked where they had gone, I helped out by moving them to the appropriate topic (ie the first topic, and the place you expected them to be in the first place).
I hope this is helpful in explaining some of our moderation decisions and capabilities.
P.S. I’ve undeleted your original question, because it’s a great question, and I’m sure others have felt the same way. So… I guess that makes more interference from the mods that is potentially confusing to you, but makes the whole site less confusing for everybody else.