There is a weird glitch in REPS that doesn’t let you delete a 2nd person. There are two options for dealing with their death.
One is to put the first name of the deceased person in parenthesis and leave it in the 2nd person box. I generally suggest putting parenthesis around the first name of anyone who dies so that everyone who looks at the record knows instantly that they have died. This way, you never lose the information about the person (like their name or birthday) but it’s very clear that they have died (as long as everyone uses this convention). Don't put the last name in parenthesis, though, because it won't show up in search results if the first character is a parenthesis.
The second option is to replace the last name of the deceased 2nd person with the word “none.” You can’t delete the entry, but you can change it to “none” so you don’t have bad data in that box.
My recommendation would be the first option, with the parenthesis, but the second option will keep your data clean too.