This is true. The 1124 will only output DC Voltages. By saying it will output only "point-by-point" this means you must continually use the software to change the output voltage. The voltage can change only as fast as your software can run. This is different from a buffered, hardware-timed output where an array of datapoints could be stored in hardware while a clock moves them out sequentially.
So I suppose you could still generate a PWM signal, but it would have to be at a very low frequency. However, you won't be able to use the 1124 if your program cannot perform point-by-point updates that keep up with the required rate.
We do have a solution as far as isolated analog waveform output. There is the
NI SCC-CO20 isolated analog output signal conditioning module which you must use with an E-Series board, but you can only get up to two channels per board.
In your case, since you just want a square wave, I would use a PCI-6602 counter board and some optical isolators.
Russell
Applications Engineer
National Instruments
http://www.ni.com/support