There is precedent in 5e for spells that do multiple types of damage. The one that most readily comes to mind is flame strike, which deals fire and radiant damage. The way flame strike handles it is it deals (for example, not sure of the exact numbers off-hand) 4d6 fire damage plus 4d6 radiant damage. This separates the two damage types to be able to apply resistance, immunity, or vulnerability as appropriate for each damage type. If you had spells that utilized multiple damage types, this would be the most appropriate way to handle it in 5e. The only problem is that it does make such a spell require more book keeping, but also reduces the possibility of it being outright resisted.
