Sure, Kakashi is present in the Boruto manga. His role might not be as prominent as in the Naruto series, but he still has significant moments and interactions.
Kakashi is very much alive in the Boruto manga. The manga doesn't include his death. Maybe you got some misinformation or confused it with another character's fate. But for sure, Kakashi is around.
Physically, Naruto can use his Rasengan or other powerful jutsus to fend off enemies attacking Boruto. His combat skills are top - notch, and he won't hesitate to engage in battle to keep Boruto safe.
In the 'boruto kills naruto fanfiction', a motive could be a power struggle. Boruto might believe that Naruto's power is holding back the village's growth or his own potential. He could think that by eliminating Naruto, he can bring about a new era of power in the Hidden Leaf. Also, it could be out of desperation. If Boruto is in a situation where he believes that killing Naruto is the only way to save someone he loves, like his mother or a friend, he might take such a drastic step.
Maybe it's the high expectations that Naruto has for Boruto. Naruto is a hero, and he might unknowingly put a lot of pressure on Boruto to follow in his footsteps. Boruto could be scared of not being able to meet those expectations.
They could start by having an honest conversation. Naruto could sit down with Boruto and just listen to his fears without judgment. This would be a first step in building a better relationship.