Yes, you can still do somewhat intelligent charging but charging in pairs you still can't insure each cell is charged exactly where it should be, Doesn't cause a lot of harm but does decrease the overall life of the cells, and if you charge in pairs over and over again the difference becomes greater each time, it adds up so you'll see shorter run time and will need to condition them more often. Thats why i say its acceptable for emergency use but don't use a pair charger all the time. If you do that and one cell starts to get weaker then when an emergency comes up you'll already be starting out in poor condition.
Individual chargers are cheap enough now a days there is no reason to charge in pairs. I'd buy a small individual charger such as the c401fs which can run from 12v in and get a panel that puts out 12v. Decent chargers make all the difference in the world, I have 10 year old NiMH's that out last brand new "15 minute charge" ones.