If the swords have any new growth showing, they are probably just converting and will be fine. Here is a short explanation: http://www.freshwateraquariumplants....ntsgrowth.html
One of the nice things about a small bowl/tank is the ease with which mistakes can be corrected - or even scrapped and restarted. That said, you may be able to gently remove the dracaena without too much disturbance, and clean up with a water change and possibly a bit more gravel. I tend to cut off unwanted plants at ground level rather than uproot them.
As for your soil depth, if you have two swords in that small of an area I don't see how you will have an anaerobic problem. More likely, you will be busy pruning the swords so they don't fill the whole bowl. The shrimp won't mind, they like a lot of vegetation.
If you do get gas building up in the soil it can be released with a chopstick or bamboo skewer. If it doesn't smell bad it is CO2 (beneficial) from normal decomposition. If the bubbles smell bad they are hydrogen sulfide. Poke around with your skewer to release the gas and consider a water change, especially if the bubbles released soil into the water column.
I think a key to success with NPTs is to have the patience to wait out the inevitable start up issues. A little time, a few water changes, and you will probably have the lovely little ecosystem you desire.