Unfortunately no, you can't charge two batteries from the same source at the same time as getting output from the two batteries in series. The only way that you could do it would be to use two isolated power supplies.
If you are not too bothered about the charge speed, you could use a couple of 1W isolated dc-dc converters... that would supply about 200mA charge current, so 10 hours to charge a 2000mAH 18650.