Hi mirza,
You do not have to use NIOS II processors with the ALTGX component. You can configure the devices into BASIC mode and use whatever protocol you like over the cables.
You will however have to be careful about the data you send over the cables. For example, the receiver CDR PLLs start in lock-to-reference mode, and then need to transition to lock-to-data mode to capture the data correctly over all process, voltage, and temperature (PVT) variations. 1.6Gbps is fairly slow though, so you will have good timing margin.
Have you purchased a development kit or two? Samtec sell PCIe edge connector to SMA adapter boards. You could use those adapters to connect transceivers on a single Cyclone IV GX Development board or on a couple of boards. If you're interested in the part number, ask, and I'll post the data sheet.
As far as 'standard' cables go. There is a PCIe standard for external cabling. You can use x1, x4 or x8 cables. There are also SFP+ and QSFP+ cables used for 10GbE and 40GbE. The 'direct attach' versions of these cables are copper, are under $100, and are rated to 10Gbps per lane, hence, more than fast enough for your application.
Cheers,
Dave