I've checked with the people who would know and can say authoritatively that USB Blaster is not being obsoleted. If it was then there would be a product discontinuation notice on the Altera website.
--- Quote Start ---
Needless to say, that a documented programmer frontend interface to the Altera JTAG stack would be the preferred alternative...
--- Quote End ---
There is no supported interface to jtag_client.dll, but if you talk to your FAE you may be able to get documentation about it.
Also, you might want to take a look at the schematics for the Stratix/Arria/Cyclone V boards, (eg
http://www.altera.com/products/devkits/altera/kit-cyclone-v-gx.html) - these have an On-Board USB-Blaster II which runs JTAG at 24Mhz and provides a ~220Mb/s dedicated debug interface for SystemConsole to talk to the FPGA.