I wouldn't worry about the drive being incompatible with the motor in this way (although there are other ways in which the drive could be incompatible with the motor -- voltage, current, phases, etc.). The drive has no way of "knowing" how many steps per revolution the motor has, nor does it "care".
It is important to understand the concepts behind the terminology. A "200-step" 2-phase motor is a 100-pole motor -- it has 50 north/south pole-pairs per revolution. In the simplest way of driving it, called "full stepping", there are 4 "steps" per pole-pair (A+B0, A0B+, A-B0, A0B-). Traditional stepper drives would transition from one of these states to the next every time they received a pulse input from an indexer.
As fsmyth pointed out, it is now often economical to create more setpoints within a pole-pair of the motor. Instead of just switching current on/off in phases, they apportion current in the phases. Think of Phase A becoming "sine" and Phase B becoming "cosine", with the resulting angle within the pole-pair's electrical cycle (1 electrical cycle = 7.2 mechanical degrees) being the arctangent of these values.
If your drive is advertised as a "1000-step" drive, it probably means that it generates 5 "mini-steps" per full step of a motor (20 per electrical cycle), so that on the most common type of stepper motor (the type you have), it can resolve a mechanical revolution into 1000 parts (0.36 mech deg). For each pulse that it receives, it advances its phasing by 18 electrical degrees (1/20 elec cycle). You should look a little more deeply into the drive literature to see that this is indeed the case.
So I think you are looking at what is commonly called a "mini-stepping" drive. Drives that create hundreds or thousands of increments per electrical cycle are commonly calle "micro-stepping" drives.
I see no reason why you could not use this drive for the motor if it is otherwise compatible, but you will need to generate 5 pulses for every 1 that you would generate in full stepping mode.
Curt Wilson
