Well, you "intelligent" charger isn't quite so smart, is it.
They are hard to find but it's still possible to buy chargers that can charge single cells or any number of cells up to 4 or whatever. I got one from Wally World a few years ago. Radio Shack might still stock one that can handle C's and D'c along with the AA's and AAA's. Get one.
When you charge cells in series one cell will be undercharged and/or the other cell will be overcharged.
That said, if you routinely use cells in pairs, you can make a case for ALWAYS charging them in series. When you discharge the "weaker" cell might actually be "reversed" charge when it runs out of juice while the "strong" cell is doing just fine, thank you.