OP, I think you need to acknowledge that she wouldn't be doing it if she wasn't enjoying it - she has a choice, so she clearly thinks what she gets out of the exercise is worth the pain/tiredness. So I think you need to leave off the paternalistic "I just want what's best for her" bit (she's a grown adult, she decides what's best for her) and have an honest conversation, first with her and then with yourself, about what problems her fitness regimen is causing you and what you want her to do to make you happier. Own your needs and foreground them rather than trying to get what you want without having to ask for it, in order to appear all selfless and concerned.
A possible opener:
"I know you love your fitness training, and that is great. However, I am feeling lonely/neglected/would like more sex/whatever your actual problem is. I would like us to spend x number of evenings together a week in the normal run of things, to relax together and give us a chance to be intimate. Are you willing to do this, and what can we both do to make sure it happens?"
If she's not willing, then you have a larger problem than just exercise and the relationship could use realigning or reconsidering. If she is, really listen to her suggestions about what BOTH of you could do to make it happen - you may be surprised to learn her perception of the balance of work/free time in your household is not the same as yours!
Fundamentally, it seems like she is probably very unhappy about your infertility as a couple and is trying to find something to focus on that takes her mind off it. That conversation should also happen, but not as a precursor to taking away her coping mechanism, just as an opportunity to offer support/compassion. If you are not as invested in solving that problem as she is (you already have a child, and talk about 'she wants a child' rather than 'we want a child') she may be feeling alone in her struggle and disconnected from you, which may have a bearing on why she seems reluctant to make time for you.
But yeah, the most important thing is to own your feelings and wishes and stop passive-aggressively making it about your slightly disingenuous-sounding concern for her wellbeing. If I were her that would be getting my back right up. I'm not her of course, I consider waddling to the biscuit tin enough exercise for any given week 