I'm using one of these card readers (I think it's the -50B) on an A2000 with a 2091 with no issues. Not really sure what the problem could be. I have LUNs disabled so only the PCMCIA slot works, which I use with a CF adapter. With LUNs enabled, the machine takes far, far longer to boot - longer than I have patience for

- since it polls each LUN at each SCSI address. My 2091 has 2MB of RAM installed and the system is also using a 2630 accelerator with 4MB. I don't remember my jumper settings on the card reader, but presumably I have termination enabled since it is the only SCSI device in the machine. I have nothing connected to the external SCSI port.
It sounds like you are able to boot from floppy and insert the CF drive afterwards to work on it in HDToolbox? Are there any filesystems installed in the RDB? Maybe the system is getting hung up on something there. SCSI reselection may be another flag worth investigating.
Are the v7 ROMs installed correctly (i.e., not accidentally swapped)? What revision DMAC chip is in your 2091? What revision SCSI chip?