I don't argue that this make cons real mainline squad. But totally remove entire unit for this, it give less diversity to gameplay. Much easier balance only one unit to another, but we all also want to see diversity and variable tactics. If you remove penals who will build T1 for SU? It will be totaly dead building without any real options (only if you want sniper for some reasons...). And don't forget that problem with cons was not only they weakness against other infantry as weak maxims do that. You always go to T2 for maxims and after maxim nerf we got penals with AT option to get buildorder where you can build infantry and get some AT options.
The consequences of the initial design: in T1 it was supposed to build shock troops and the Guard if you chose the appropriate commanders, they replaced the penals. The concept was gone, the design remained. Penalties were originally a unit that was unnecessary.
To fill the void in T1, can be added there broneboyshchiki (anti-tank riflemen) 4 conscripts armies with PTRS, camouflage and AT abilities .