Is the free Xilinx ISE webpack provided by Xilinx usable with this SDR-2 kit?
No, it isn't.
The Xilinx webpack supports only small FPGA devices.
It is required to use the Xilinx ISE Foundation software to access the SDR-2 Virtex-4 FX60 FPGA devices.
What software for SDR-2 kit is available under MATLAB?
There are full support from: SMT6040, SMT6041, PARS and even MATLAB/Simulink Real Time Workshop, Simulink HDL-coder and Xilinx System Generator that are fully compatible with the 3L Diamond tools.
Other design approaches are available like "C-to-FPGA" compilers like Impulse-C.