Not reading thread, putting in my two bits nonetheless.
I don't know how it works in other branches, this is speaking strictly from the viewpoint of the USMC:
As it stands there are different fitness requirements for males and females. Until this year females didn't have to do pullups for the Physical Fitness Test, they did a timed flex-arm hang. They are implementing a pushup requirement but their minimum standards and max scores are lower. Their run times are allowed to be higher (despite the classic thought that women should be faster, for some reason). It's the same for the Combat Fitness Test. Note that in addition to a different standards for sex, there is also a different standard for age. The requirements for a Marine - male or female - age 27 to something is lower than those 18-26 (I might be off one or two years). There's at least one other bracket above that age group and a final one at 46+.
There is, however, absolutely no difference in PFT/CFT requirements based on MOS. The yearly tests are across the board. For certain "elite" jobs like Force Recon and Scout/Snipers there requirements to get the job and stay in it are higher but only in the sense that you have to score a certain level (1st class) on the very same PFT/CFT that everyone else takes. Force Recon usually requires stronger swimmers but even then the requirements are based off the same swim quals that
everyone takes.
Those are special cases, however. The official physical fitness requirements for an admin clerk or legal aid are identical to the official physical fitness requirements for a rifleman, machine gunner, mortarman, and every other kind of grunt. A 98lb weakling serving in the infantry might be tossed into the admin shop to keep his deficiencies from getting in the way but at long as he's scoring the bare minimum in the PFT/CFT there is no way for the Marine Corps to say "you can't run fast enough for this job, you need to be tranferred to something else". The problem is that if this becomes a common practice with females in the infantry then you're going to have an admin shop full of females complaining that they're not getting a fair shot.
As for women currently in combat: there is no "front line" and there hasn't been for ten years. Truck drivers and cooks and paper pushers of both sexes have found themselves in firefights because that's how the enemy wants it. There are also Female Engagement Teams/lioness/whatever they call themselves these days that routinely go out on patrols. Some people say they ones they've worked with were shit hot and put the male grunts to shame, some people say they were worse than useless and made it the most dangerous babysitting job in the world.
If rape is a problem then the problem is the people who would rape. Someone who would do that should not be given a weapon, should not be wearing a uniform, and should not be representing our country to a culture we're trying to get on our side. That being said, it will happen. It already does. They have to show commercials on AFN reminding us not to rape each other. There's a serious problem in that regard but the solution to that is not "don't give the rapists more opportunities" it's "eliminate the rapists".
There are not nearly as many women capable of meeting the physical requirements as males. There are plenty who can do it, there are plenty of men who can't. There are plenty of chicks that'll out run, out shoot, out ruck, out lead the rest of the pack. But they are less common than the average male who can make the cut. Keep in mind, however, that with the severe draw downs going on they can be far more selective on both fronts. We no longer have to deal with pushing shitbags through boot camp to meet numbers, no need to tolerate fat or stupid turds in the fleet that should have been let go because the op tempo is too rapid to get replacements in time. They can weed them out but they need to raise the standards, they need to ensure that those who are in those jobs are top notch regardless of the style of genitals they came with.
Regarding the hygiene thing, it can be a problem but in this era you can carry a pack or two of 20 baby wipes. It'll fit in a cargo pocket along with tampons/pads. Not a big deal.
There's the argument that men won't be able to suppress their instinct to save a woman. It's a stupid argument. Not only are grunts surpressing the most basic and primal instinct any living creature has - self preservation - every single day but plenty of grunts have had to shoot female insurgents or IED mules in the head as necessary to save lives or accomplish the mission. Do people really think that "protect the female" instinct only applies to those of the same nationality? It's the same level of nonsense as when people were saying that it would be too distracting to have a gay dude fighting next to you.
I don't think our culture is mature enough for a completely unisex military a la starship troopers or BSG, but it will eventually happen. Just like DADT ending eventually happened. It won't hamper our ability to fight. It might cause friction in the short term but ultimately the goal of an equal society is the greater good. We can't claim to be fighting for American values if we refuse to uphold them
while fighting.