Yeah, Maka and Soul developed a lot during just during the beginning of the main series, let alone towards the end. I'm sure they have actually hunted some twisted souls already in this series' time (because they had 98 when the main series launched), but it's totally different to try to stop somebody without causing any damage. Maka is also purely book smart, so if they haven't been taught how to restrain a berserk weapon, instead of liberating the soul for a weapon to eat (that is, kill), she can't do it.

We would have needed either Black Star or Kid here. Eternal Feather would have been down for the count in a second, without the need to even use a weapon.