From reading the spoilers, I didn't get that impression. She is extremely concerned about him and I think she will be there when he wakes up. One of the scenes has her at his bedside like he was at hers in SGIYC. I think whatever "strains" their relationship will happen when he wakes up after coming out of the coma.
Obvously something is said between them that leads to the apparent estrangment in ep 802. I honestly get the feeling that the "break" is his idea. There are soo many possibilities as to why this break happens and honestly all of them, imo, are cliched. I think it comes down a couple of possible scenarios if it is he who initiates the "break":
1) He is upset she shot at him and feels the trust is no longer there and maybe his injury has some lasting affects and he blames her ( I think a version or variation of this one is the biggest possibility which imo is childish on his part b/c how could she have known he was in the car?)
2) He has some amnesia and doesn't remember they were together and simply goes about healing not realizing he is hurting her.
3) He feels guilty he put her in that position in the first place and pulls away out of guilt. (I could see this one too b/c he was so gung ho about ignoring the rules in order to be together while she was hesitant b/c of the rules...ie the season 5 finale conversation. A little role reversal if you will.)
4) He is in trouble with IAB for helping his dad and doesn't want her to go down with him...he is trying to protect her and therefore pulls away.
The fact that Natalia says "he sounded worried" to Cal in regards to Eric calling her to ask about Cal's wellbeing and Cal being sad that he didn't call her really gives me the impression that
he is the one who initiated, in some way, the "break." Why would she add the "he sounded worried" if, in some way, he wasn't supposed to be upset with her or separated from her?
Regardless of his reasons for pulling away, I am very sure that there will be some really big cliched moment that will bring them back together. I highly doubt the writers will simply decide to have one of them approach the other and decide that they need to "talk" about thier situation. Their relationship has never about going the "easy" route....So I highly doubt any situation to bring them back together, will be uneventfull and simple.
This is just my impression of it all anyway