The only supported way is by scripting of Altera tools which is probably no suitable for doing what you want to achieve. The Quartus JTAG client driver has of course interfaces, that would allow to access EPCS either in AS or indirect JTAG mode. But they are undocumented.
The USB Blaster can be also accessed directly through FT2XX.dll. But you have to understand the operation of the USB Blaster SERDES CPLD. It's not documented by Altera, but there are sources on the internet. It's basically easy.
Another way would be to use a naked FT2232 as JTAG interface. It would be also supported by commercial tools as TopJTAG (
http://www.topjtag.com). And it can be operated as a USB Blaster replacement by the BeMicro USB Blaster driver.
