Eh, looks like it's time for me to engage in my semi-annual
partial defense of Fo4. It's a dirty job, but someone's gotta do it.
Which is part of the problem with Fallout 4's plot. Right out of the gate, they shoehorn you in to the role of being a parent with a new born. They went even further by establishing the background for both the male and female character, which has no tie in with the game beyond, "This is Dick and Nora's background!"
This is part of Bethesda's differing strategies for their Elder Scrolls and Fallout IPs. The former is their freeform roleplaying sandbox, whereas with the latter they tried to move towards tighter storytelling aided by a predefined PC, as we saw in both Fo3 and Fo4. They
failed, because Bethesda's allergic to Microsoft Word and every other implement of literary expression, but that's the idea behind the structure.
It's a business strategy to diversify your portfolio and cover more ground, as some players will prefer freeform characters, others want stronger drama. CDPR tried to do the reverse, moving from The Witcher, centred on, uh,
the witcher, to Cyberpunk's more open protagonist... and they also failed, with V feeling even more restrictive than Geralt, albeit for different reasons.
It gets even more stupid at the cryo vault when they shoot your spouse once you realize what the plot is. In fact, it's stupid they didn't take EVERYONE from that vault given the plot. It's not like the Enclave in Fallout 2 didn't take everyone from Vault 13 and everyone from Arroyo.
This isn't that egregious as plot holes go. The Institute's priority is only the infant at the time, the PC is specifically referred to as "
the backup" and successfully put back on ice, though there is a legitimate question why the other spouse doesn't get similar consideration. Kellogg shooting them could be passed off as losing his temper, but it would be at odds with the rest of his characterisation so the absence of an explanation is a mark against Bethesda.
I don't recall whether the rest of the cryo subjects had already expired or they did so later, as a result of the Institute's tampering, but they clearly weren't relevant to that project and Vault 111 was already a pretty secure refrigerator for the one remaining backup. The safest play would've indeed been to take the other spouse too, but maybe they wanted to keep them pickled and didn't have cryo tubes lying around at home, you can come up with passable excuses.