You can save the signal you're scoping as .wav file and use wavread in matlab. Its not as simple to use as the simulink one because you have to use a little sense to set it up. IE sampling rate, and if you choose to do an FFT you'll have to do a little extra work there as well.
But just command line matlab will work just fine. It will do everything you need if you're aware of what the functions you need.
OH and it won't be "real time." In some cases that might matter, but I'd think in most cases it won't. Other than if you're making a lot of changes on the fly it'll be pretty annoying.
There are also a lot of free oscilloscope programs as well.
And just to comment on anything below 4 decimal places getting rounded: Yes it'll be rounded, your sound card doesn't support that type of time resolution its limited to something like 44khz sampling rate, if you want anything higher you'll have to buy a digitizer.