A delta T of 50 deg C will probably be ok.
The shear stresses in these sort of joints peak at the ends, typically over the last inch or two. (Depends heavily on relative stiffnesses of the substrates, the glue shear modulus and the glue line thickness.) Thus cutting the aluminium into six inch segements probably won't help. You'd probably need even shorter lengths. To quantify the critical length for peaking you need to do a little stiffness analysis, preferably with FE. There ought to be some little formulas for doing it by hand, but I've never found any.
If you've got equal-ish stiffness-times-areas of ally and carbon then they'll both strain the same amount and the total relative length change will be half the difference in the two CTE*delta-T's. This is the best possible situation.
If one material totally dominates the EA then the total length change will be the difference in CTE*delta T. Thus, if the carbon laminate has a CTE of 3e-6/deg C and the ally is 24e-6/C, the worst case strain (say the panels dominate) is 21e-6*50 = 0.00105 tensile in the aluminum. It won't be quite that bad, because the panels will be shrunk a bit by the aluminum pulling on them. Anyway, a strain of 0.00105 translates to a stress of 0.00105*10.5e6 = 11 ksi.
Now, assume the angles are 0.02" thick and have legs 1" long. That gives a cross-sectional area of 0.04 in^2. With a stress of 11 ksi this will generate a force of 0.04*11000 = 440 lb. This will be reacted with some sort of distribution at the end of the joint. Assume it is reacted over the end one half inch. Shear area is 0.5*(1+1) = 1 inch square. Total shear stress would then be 440/1.0 = 440 psi. A good adhesive will have a shear strength of at least 2000 psi.
If you're just looking to the aluminum to protect the carbon then it's probably a bit OTT. A thermoplastic would probably be cheaper and lighter. However, if you're also using the ally to join the panels together then it's a reasonable choice.
With regard to insulating the metal from the carbon, it's usual to put a layer of glass scrim in the laminate in way of the metal, but it depends on your service environment. If it's indoors then you'll almost certainly be ok with just the adhesive and the primer on the metal. It's not as if you've got any fasteners potentially making a circuit with actual fiber contact.