Terrain maps require active radar. Active radar increases your detectability.
> If you are using terrain maps to navigate, then you don't need GPS - so this system has no hopes of working against low altitude cruise missiles.
Some currently deployed US Navy Cruise Missiles already utilise GPS. Including the Block III TLAM[0].
They support INS (inaccurate), TERCOM (which has a radar signature), and DSMAC (which relies on TERCOM or GPS, and only increases final target accuracy).
You'd definitely use GPS if you could use GPS, it is the most reliable and quietest system. This system proposes to neuter your ability to use GPS in Russian territory.
> Also, the cruise missiles would need to be flying lower than the cell towers
That isn't how radio signals work.
[0] http://www.navy.mil/navydata/fact_display.asp?cid=2200&tid=1...