Oh man, you had me worried for a minute there. Like, almost pissed at yet another thing nullified for my beloved Deathwing army with the new 'dex.
Right until I read the caveat '1' (pg.97, bottom right in italics) which applies solely to the CML:
Does not replace the model's storm bolter.
So you can swap all your weapons for a TH/SS as per the entry, then take one item from the Terminator Heavy Weapon list which doesn't need to replace any weapons. The way I read it,
1) DW Terminator comes with SB/PF base
2) swaps SB/PF for TH/SS (all stock weapons have been replaced)
3) 5 models in the squad unlocks an item from the THW list
4) model with TH/SS takes CML as it is the only weapon that doesn't swap out the SB
I know the vernacular is subtly different than in the old book, but does that jive with you?