If the card reader supports hot swapping, then yes.
The card reader would need to support the ATAPI protocol, which many of the very cheap IDE card readers do not (they are a passive adapter between the IDE cable and the CF card, without the active electronics to support the ATAPI protocol).
The cheaper IDE card readers, without ATAPI, are not hot swap, so the card has to be kept in the reader from when it is powered up, it can't be swapped with another card while the power is on.