Well, most Missiles being bad at Anti-Tank is not a balance issue of the Tabletop, it is intended. Missile Launchers are a universal gun, decent against vehicles and infantry, thanks to their choice of ammunition. But for that variety they are no ace in any of that category. In the TT HKM is just a Krak-Missile with unlimited range and that rightfully so fr it is no magical anti-tank weapon. It is the primary weapon of no vehicle at all, and making is nearly as strong as a Lascannon would also not fit the setting.
Also if this one-shot gun that probably requires a Techpriest to reload after a Battle is so important to your Mission, maybe change the overall encounter a bit? There is always a chance that they fire the Missile before they even get to the Leman Russ, even more so there is a chance that they will miss that thing or cause that little damage that nothing at all happens. Reliance on a one-shot-only gun for an entire encounter that is strong enough to cause an entire wipe is maybe not a good approach. after all. And because the PCs are off the Death Korps they cant even retreat and gladly accept to burn a Fate Point.
SO if you are willed to change the entire start of the campaign that was nothing else that army consolidation, digging and building some trains maybe some minor changes to vehicle load-out wont hurt either. At last give them tons of melta-bombs or satchel charges so they can make some suicide bomb-run before they get smashed.