Let's say that TH is 100% factually innocent. She could have felt a lot of guilt, and/or worry that the rest of the family would blame her since Kyron was last under her care, custody, and control.
To top it off, she may have secrets (like the landscaper) that she does not want the rest of the parents to find out about, that she believes have nothing to do with Kryon's disappearance and might even cause suspicion (like the landscaper).
Trouble is, even with that, I don't see how someone who has a significant parental role in raising a child would feel
persecuted by the investigators in this situation.
From 
 
http://dictionary.reference.com/browse/persecute
Persecute means:
1. to pursue with harassing or oppressive treatment, esp.because of religion, race, or beliefs; harass persistently.
2. to annoy or trouble persistently.
I would like to be troubled persistently if it would help find a missing child, unless I had something significant to hide. It doesn't mean I would enjoy relinquishing any secrets I had, but relinquish them I would because that would be far less important to me than finding the child.
Also, if I were innocent, I would proclaim that loudly and persistently to anyone who would listen.
I agree. Here's the thing. There is just one thing after another that keeps coming out pointing to guilt, IMO, especially if all is eventually substantiated by LE. It is beginning to remind me of the casey anthony case. The parents made an excuse for each fact that came out as if each one of those facts was in a vacuum. To me, it's the cumulation:
1. She is alleged to have hired a hit.
2. She was the last one to see Kyron.
3. We have yet to see an account of where Th was between 8:45 a.m. and 1:45 p.m. the day Kyron disappeared.
4. She reportedly walked out on a second poly and failed two.
5. She showed defensiveness, in one man's opinion, a man who happens to be an investigator, in a manner that was not normal.
6. The bio-mother's gut is that TH did something.
7. She has refused to speak with investigators of late and hired a famed criminal defense attorney, a step many guilty parties take.
8. Instead of grieving, searching, screaming for help due to the disappearance of her lost son, she reportedly engaged in a sexual exchange with her husband's friend, in the
days after her son disappeared.
9. She tried to take her daughter in a secret manner at the moment she probably knew the you know what was about to hit the fan with her husband, instead of directly confronting him and stating she was taking her kid.
10. Her husband filed for divorce and applied for a DV RO stating that LE had provided probable cause that Th was involved in Kyron's disappearance. The temporary RO was granted and not so much as supervised visitation was given to TH with her infant daughter.
11. TH does not seem to be fighting the RO, including the no contact request with her baby girl. This, among all other things, says the most to me. If innocent, she would have zero reason to fear testifying and refuting the allegations in civil court. If innocent, no attorney could persuade her to give up contact with her infant. On the flip side, if guilty, a civil hearing at which she must refute the allegations against her about Kyron, she would incriminate herself. Anything she said or did would be used against her in the criminal investigation and a possible trial. She CANNOT fight the charges if guilty. As a mother, nothing would stop me from fighting the charges and getting my little baby back in my arms, if I was innocent.
Although it's not one thing that can be excused in some manner, that last point is the one thing that, in the absence of anything else, would tell me, as an attorney, she did something. But there is not just one thing. It's a whole, huge bag of stuff that just keeps getting worse.