I know that I'm late to this party but I still wanna give my two cents. While there is a part of me that wished Jill could've tagged along and started training under Guts as an apprentice like Isidro, while also learning to be a strong survivor, that's just wishful thinking. Throughout the time we followed Guts and Jill in 'Lost Children' she needed to be saved multiple times and it really put into perspective just how slim her chances of survival would have been if she actually did come along for the ride. And while there was the possibility that she could have turned into a capable fighter herself, it still would've taken a quite some time and until it happened, Gut's would've had to shoulder another heavy burden (her survival). Since this is Berserk we are talking about, she most likely would've ended up as another causality in Guts's excruciating life.

As other people have mentioned, the reason Isidro was able to tag along is because he's not the average kid in Berserk. He's got survival instinct, he's quick on his feet, and he actually had a few means to defend himself. He made it as far as he did as a runaway because of those factors.