what bandwith is the connection between the two sections? If it can be done via DC-Cabling with high bandwith I'd do the following:
As the mediaagents are responsible for controlling the backupstorage, I'd place them in the same section as the backupstorage.
If section 1 (OnlineStorage + Servers) goes down you should still be able to restore the data.
Just my 2 Cents.