Standing Wave Ratio(SWR) Measurement
To measure VSWR of a load accurately, you need to measure two things: The power outbound toward the load, and the reflected power returning from the load.

The reason for measuring the outward going power is that many generators will change their output capability slightly, depending on the reflections coming back from the load. For example, in your setup, the filter that's converting your 10 MHz square wave to a sine wave is likely to change it's characteristics depending on the effective load impedance it is seeing.

In order to measure the outward and inward-travelling signals separately, it's usual to use a directional coupler, or a combination of directional couplers. 

You can buy a reasonably-specified pcb-mount directional coupler from a company like Mini-Circuits, or, particularly since you are interested only in 10 MHz or a narrow range of frequencies around it, you may be able to construct one(PDF link) yourslef.

Having separated the the forward and reverse signals, you should consider rectifying each one with an rf detector rather than sampling directly with a fast A/D. The detector will convert each signal to a "dc" level which can be sampled with a low-speed, low-cost A/D.