Since Leatherhead was there with them, he was able to hold off Kirby long enough for Splinter and Tang Shen to take notice before he could kidnap April.
Instead of using the Subspacial Endoparticle Disrupter on the portal straight away, Donnie uploads a virus to bring down the force field.
Freudian Excuse: While canon!Splinter claims that he doesn't join his sons into battle because he wants them to be self-reliant, here there is another reason: Tang Shen survived that night against the Shredder with wounds that left her weakened. While he trusts his sons to defend themselves, he stays to protect his wife.
Spotting the Thread: While April has her doubts, Leatherhead immediately realizes that there is something wrong with Kirby when he refers to the Hamato Children as "The Kids" the same as the Kraang.
