I am not new to integrating new chickens, but I also have never had a rooster involved in the equation. I have (7) six month old chickens (1 is a rooster). I have (7) seven week old pullets
At 6 months he isn't a fully mature rooster and the girls are probably not acting as mature hens yet. Their relative immaturity might be contributing to the problem. I like having a mature rooster in the flock when I integrate young chicks, my mature roosters tend to ignore the chicks but sometimes help take care of them. I think mature hens are less of a risk than immature pullets but less doesn't mean zero. That is not exactly what you are seeing.
In the past week or so, I have let them out of their pen to run freely and to observe behavior from the older ones. The babies get pecked at by my hens, but doesn't seem too aggressive. The rooster (who is actually a pretty good boy) does peck at them harder than the hens do, but at least he seems like it's more of a "don't come in my space" kind of peck.
I assume this behavior takes place outside in the run. How big, in feet, is your run? A photo might help. What generally happens with mine is that immature chicks are likely to get pecked if they invade the personal space of the mature chickens, especially the hens. It doesn't take them long to learn to not invade that personal space. That sounds like what is happening. Mine generally form a separate sub-flock avoiding the adults. The older go wherever they wish, it's the chicks that have to avoid the older. Do yours have enough room to avoid or are they getting trapped in a dead end?
I have no where else to put the babies at night, so I bring them in my house at dusk to sleep in their brooder and take them back outside early in the morning....... they NEED TO BE OUT OF THE HOUSE -
I totally understand. How big is your coop in feet? Photos inside might help. Luckily they are old enough and acclimated so that cold weather is not a factor.
You could build a pen in the coop and house them in there for a week or so. The main purpose of that would be to teach them to go to bed in there when it gets dark. If the other method doesn't work this could be a fallback to get them out of your house.
The way I approach this is to lock the chicks in the main coop with the adults after they have shown they can roam outside together without getting attacked. I've had a couple of broody hens wean their chicks as young as three weeks, leaving them to make their way with the flock on their own. My brooder is in the coop so those chicks are raised with the flock. Those are making their way with the flock by 5 weeks. You didn't manage yours that way but the see but don't touch you've done is close. I have over 3,000 square feet outside they can roam so room is not a problem, they can easily avoid the older ones.
It can help to avoid conflict if you have multiple widely separated feeding and watering stations. You can improve the quality of what room you have by adding "clutter". Clutter means stuff they can get under, behind, or over so they can break eye contact. That's one reason photos might help with specific suggestions.
I wait until dark and put the chicks on the coop floor if they try to sleep outside. The older ones are already on the roosts and it is too dark for them to attack the chicks. My brooder raised chicks typically don't start roosting until they are a few weeks older than yours anyway. Until then they typically sleep on the coop floor. When they do start to roost it's usually not with the adults anyway. I don't care where mine sleep as long as it is with predator protection and not in the nests. I put an additional roost lower than the main roosts by about a foot, horizontally separated from the main roosts by over 3 feet, and higher than the nests to give them a safe place to go when they start to roost.
If it is dark inside the coop they should be safe from the adults until it gets light. So I'm down there at daybreak every morning until I'm comfortable there won't be a problem. I just open the door so they can get outside where there is more room. What I typically find is that the chicks are up on the roosts avoiding the adults that are walking on the coop floor.
Usually my pullets stay in a sub-flock and avoid the adults until they start to lay. That seems to be the signal that the older hens will accept them as equals. Of course there are exceptions to this, there always are exceptions. Sometimes they intermingle a lot more at a younger age than I make it sound. It's a process, not an overnight thing. I typically advise to base your decisions on what you see, not what somebody over the internet like me tells you that you will see. We all have different flocks with different personalities and makeups, different facilities, and different management techniques. We get different results. Hopefully this will help you determine a way forward with yours. Good luck!
I have a similar situation with 11 seven week olds and 5 seven month olds. I'm going to remove my brooder that's in the run and place them in a wire crate inside the coop at night for the next week. 
