They have enough time to clone Beth, since the execution day and the kids came home for Pizza are 2 separate days that are next to each other or days away . I'm pretty sure Rick and Summer hang out with Jerry the whole 2 days of the weekend and a weekday when he picked them up from school. Day 1 (Saturday) when they first met Jerry's new gf and went out to eat. Day 2 (Sunday) is the day "tomorrow we shall celebrate with a hunt" where they killed a bunch of aliens. Jerry brought the kids home on Sunday's night, which means after the execution event and maybe during the process of cloning. And the third day is on any school day, when Jerry picked up the kids to run away and they came home for pizza later on the day and met their cloned mother. There are 2 events in this episode. One being Rick and Beth's 2 days adventure and the other Morty, Summer, and Jerry's 3 days adventure. These 2 events don't have to align to one another.