In everything I write below, I will neither be trying to assign blame, or to demonize; but to describe to you what is going on, and to point out possible avenues of betterment. Keep that in mind.
I allowed him to continue because when I don't, he starts with the script as I typed above. He continued to penetrate me to climax, despite that I was distant, still weepy, and could not look at him. In the middle he stopped to ask me "You just aren't going to get back in the mood I guess?" I said no. When he finished he tossed me a towel and went to shower.
I don't need to tell you how catastrophic this is. No matter how big or small fish in how big or small pond, no matter how much sympathy one may have for the divergence in libido or his stressful job, this behaviour of his transgresses many, too many limits, and while you may have consented in the interest of "peace" then, it must not be repeated.
You will need to protect yourself, if he will not have the consideration to notice your limits. To this end, I urge you to seek out cousneling, on your own, to learn how to protect yourself.
I don't know how long it's been going on, but over time, my husband has taken to negotiating sex when I say no. It goes something like this:
That is common behaviour. Your husband is just as resentful as you are. To him, sex is likely one of the few refuges he has from stress, and he wants pleasure and intimacy; and he's likely resentful because the sex-hungry bride he married has been replaced by a tired, stressed out mother. Your willingness to help him out does you great honour, but it is not enough, it is not what he is seeking.
He tries to negotiate / nag, because he knows what if he does not, there will be even less sex. There will be no quick fix for this. In the long run, you will need to learn how to reconnect with the sexuality you lost after the birth of your youngest child - through, again, counseling. It is hardly your fault that you don't feel sexy with the stress and the kids and the sexual assault; but for your own sake, you should seek help so as to not let your sexuality become this shrivelled appendix of your personality. You need to learn how to make room and time for you to be sexual again, to orgasm (if only by yourself!) again, to be a whole woman again - and you need to learn how to command others to support you in making room and time.
My husband is a trauma surgeon who is up before dawn and comes home at dusk.
That tells the whole story.
Emergency help providers like him, and specifically emergency medical professionals, are under enormous emotional stress. None of them manage to perfectly separate the psychological assault they undergo every day at work from their private lives entirely; and few of them manage to stop the slow ulceration of the heart that leads to a staggering decrease in empathy.
How so? Because the barriers they throw up to protect themselves against what they see slowly overtake their personality; because they are extremely hesitant to accept psychological coaching (how often does your husband undergo supervision a month? - don't answer :D) for the fear of seeming weak; because they have ready access to "little pickmeups" that help them over the stress and emotional injury, and these pickmeups only erode the personality further; and because the esprit-de-corps in their profession reinforces and sanctions all that.
Your husband, willing to accept it or not, is in urgent need of counseling, too, and for his own sake.
I know he's got women throwing themself at him (he's very attractive and is a doctor)
You are putting yourself under sexual duress. Yes, he may have women throwing themselves at him, but that is no reason for you to coerce yourself into sex you do not want. Unempathetic (and, in the incident you narrate, brutal) though he maybe, the coercion is being done by yourself!
That too, deserves the attention of a professional counsellor.
All said and done, there is yet hope. But to realize that hope,
you must urgently learn to protect yourself, for your own sake, husband or no husband
you two must work at your mutual resentment, with external help, for the sake of both of you and your marriage
you need to reconnect with your sexual side, for your own sake, husband or no husband
you need to learn to stop coercing yourself via phantoms ("all the women throwing themselves at him"), for your own sake, husband or no husband
you need to redude the stress in your life - singular, because I know he won't be able and/or willing to reduce the stress in his.
your husband needs to learn to separate professional and private life better, to accept and call for the help available to support him in his emotionally difficult job, and to reduce his stress levels, for his own sake, wife or no wife.
All the best!