I've been summoned!
In general pretrial confinement is very unusual in the military, even for very serious crimes, and if it's imposed without a clear legal basis the prosecutor ends up paying the price. (As an aside, I once recommended to a commander that he restrict a pretrial Airman to base after he had stolen two diamonds and taken one of them to Korea to propose to his girlfriend, and the judge ended up giving him five-days-to-one-restricted against his sentence, holding that it was done without a sufficient basis - that still sticks in my craw!)
My experience has been that military jails are much cleaner and safer than their civilian counterparts. That said, solitary confinement takes a psychological toll on inmates and I don't doubt this guy is hurting. It seems to me it's reasonable to restrict his contact with others based on the nature of the offense in this situation, however.
Military members have the same speedy-trial rights as civilians - military members have to be tried within 120 days of the preferral of charges unless they waive the right. Here, he was charged in May and has been in the clink ever since, so I gather he has waived speedy trial. This is quite common.
As far as I am aware no charges have been presented to a judge in this case. The charges are initially preferred by the member's commander, then referred to an Article 32 hearing (similar to a grand jury), where a recommendation is made with respect to whether the charges should go forward. I don't believe that has happened yet in this case. Even if the Article 32 officer (an experienced JAG who may or may not be a judge) recommends that the charges be dismissed, they can still be referred to trial by the member's commander. Assuming, as in this case, that the charges are of felony-level severity, the referring commander must be a general (hence the name General Court-Martial).
The case will, most likely, end up with either a plea negotiation or a litigated trial. The defendant chooses either a trial to the judge or a trial by members (aka jury). Because Manning is enlisted he can request a panel of members consisting of no less than 1/3 enlisted members, with the rest being officers. In my experience military juries are thoughtful and generally better-educated than their civilian counterparts. I do believe it's a fair system and he will get a fair trial. This particular trial will likely be nonpublic due to the classified nature of the evidence, and the prosecutor, defense attorney and judge will all need to be people with sufficient security clearances to hear the evidence.
Interestingly, unlike pretty much any civilian jurisdiction, there are no sentencing guidelines in the military, so his minimum sentence is always no punishment, regardless of the severity of the crime - the UCMJ just imposes maximum sentences. E.g., there is a ceiling but not a floor.
If anyone's curious, Manning's actual charge sheet is at
http://www.fas.org/irp/news/2010/07/manning070510.pdf.