Oooh my god, I've racked my brain trying to know what is the correct solution to the church scene and I skipped it specifically because I couldn't make up my mind. But I'll put in my two cents now that I've checked and double-checked the material again (the Japanese script and how the scene plays out in terms of the models movements).
So here's the play by play in the Japanese unmodded version (starting immediately after naming Aerith) with quick translations of my own:
「わたし、花売りのAERITH。
よろしくね」<End> "I'm the flower seller Aerith. Nice to meet you"
(Leno walks in, Cloud and Aerith don't notice)
CLOUD
「俺はCLOUDだ」<New>
「仕事は……
仕事は『なんでも屋』だ」<End> "I'm Cloud. My job is... I'm a Jack of all trades [can be interpreted as general merchant. Literally an "Anything-er" or "Does-Anything-man"].
AERITH
「はぁ……なんでも屋さん」<End> "Woah/Oh?/Well!... a Jack/general marketer."
(Aerith starts laughing [I THINK because of the General marketer interpretation??? Or she just finds an unusual job title like Jack of All Trades/なんでも屋 amusing.])
CLOUD
「なんでもやるのさ」<End> "I'll do anything/take any job, you see."
CLOUD
「何がおかしい!
どうして笑う!」<End> "What's funny!? Why are you laughing!?"
AERITH
「ごめんなさい……でも、ね」<End> "I'm sorry... but, hey..."
(Aerith notices Leno, Cloud too.)
CLOUD
「ん……?」<End> "Huh?" [THIS DOESN'T SHOW UP IN EITHER JAPANESE OR ENGLISH VERSIONS OF THE GAMES, I ONLY SAW IT NOW IN THE SCRIPT. If it did, I think it would solve a lot of confusion. It's pretty clear this is the point where Leno is supposed to be there.]
AERITH
「CLOUD!
かまっちゃダメ!」<End>
AERITH
「タイミング、悪いなぁ」<End>
AERITH
「ねえ、CLOUD。
ボディガードも仕事のうち?」<End>
[In Hermans FF7 Script, these are in the wrong order. You can talk to Aerith and she will say 「タイミング、悪いなぁ」, before running up to Leno, which is when she says 「CLOUD!かまっちゃダメ!」. After that she says「ねえ、CLOUD。ボディガードも仕事のうち?」when you talk to her, progressing the scene. So I'll continue below with this adjusted and Leno's line added.
(If you talk to Aerith)
AERITH
「タイミング、悪いなぁ」<End> ("Bad timing, huh.")
(Cloud runs to Leno, is stopped by Aerith by : )
AERITH
「CLOUD!
かまっちゃダメ!」<End> (Cloud, don't care about it/him!)
(Cloud shrugs)
(If you talk to Leno)
[LENO]
「オレにかまうな、だと」<End> (She said, don't care about me.) [Two things that further point me to the conclusion that it's probably "Don't mind him" rather than "don't let (my laughing) get to you": Both Leno and Aerith use "kamau; to care about, to mind" and I even think Leno's verbal tic だと is used grammatically here as in だと[言った] (omitted [she said]). Meaning, Aerith had to be referring to him.]
(When you talk to Aerith)
AERITH
「ねえ、CLOUD。
ボディガードも仕事のうち?」<End> (Hey, Cloud. Is bodyguarding a thing you do?)
And the rest of the dialog is fine.
So. My conclusion is sadly I think you have to rearrange this scene again DLPB ... The evidence points much more heavily at the "timing" referring to the timing of the Turks, not Aeriths laughter, and the "don't mind him/don't let it get to you" is indeed about Leno...