Planted in June... that will give this plant a really rough summer. Could you tell me where you got the plant? Given that I live in the Phoenix area that may give me some context as to how the plant was grown in the nursery.
For landscape plants that you expect to expose to full summer sun, you should try and plant in the Fall, so they have a winter and spring to establish themselves and acclimatize to the sun.
So the sun scorching is no surprise. You probably would have had that even if you planted it in the fall - the older leaves are likely just not accustomed to the full sun.
The rot is not uncommon, but slightly strange in terms of location. It is sort of a damned if you do damned if you don't situation - if we get a strong monsoon like this year many aloes including Hercules are prone to developing crown rot (hence my comment about it being in a strange location). It is usually due to water pooling in the crown and not evaporating enough because it has been shaded so heavily, combined with high night time lows. However if you do not shade the plant in the first summer after planting it - especially since it was planted so late - it would just burn to a crisp.
A large Aloe like 'Hercules' tends to be OK more often than not the plant I had to leave at my old place branched after it had the crown rot. When my plant got it it was so tall I could do nothing about it, but one thing it had in common with yours was that it was in pretty heavy shade of a tree and it was during a relatively good monsoon year.
I worry that what I am seeing in the pictures does not look very well cleaned yet. You hate to cut off a healthy looking leave, but I would cut that leave right below the spot off and then clean any of the goo off as best as you can. Hose the area down with a strong spray and then with sterile knife cut as much of any remaining rot looking spots from the trunk.
Let dry out a bit and sprinkle with anti-fungal powder you can get at any decent nursery. Then inspect very carefully if the rot has gone any where else.
I agree with uncovering, but I would do it carefully as that looks like pretty serious shade so the plant would not be happy to go back to full sun suddenly.
At my new place I am growing one that gets morning to just after midday full sun (well it will get more and more sun as it grows) and it takes that reasonably well, with older leaves getting sun scorched every June-July so far until the monsoon hit. The first summer after I just planted it (planted in November) it started to develop crown rot. I got lucky and saw it early and removed the area and it recovered just fine, no branching this time.
Here is mine at the end of the day some time this last June, it has a weird lean that I will soon have to correct (that will be fun), but you can see the remnants of the lower leaves from the first two summers it was in the ground.