Global upgrades are anathema to mixed compositions.
Making Conscripts cheaper won't fix the fundamental design problem with global upgrades. Conscript upgrades are only cost effective if you build several squads, so there's little point mixing them into other builds.
Why would people build Conscripts when they're rewarded so heavily for not doing so?
And that is the whole point. Either you spam conscripts and you have to invest in their upgrades or you use a couple of them in a mixed force and you only by the bare essential like AT grenades.