For one, Goddess Madoka is being a benevolent existence and concept, so Touma wouldn't want to mess with her.
If anything, having her as an ally would blow Touma's mind even more so than the thought of having to destroy her.
I haven't thought much about him seeing Hyouka appearing as an ally that went to fight
freaking Archangel Gabriel on a somewhat even footing, but knowing Touma, and applying the same thought process on Madoka as well, he'd rather deliver his fist personally to whoever is causing trouble than having Madoka deal with it.
Just my two cents.
Oh, and another thought crosses my mind.
Touma, being the cosmic plaything, wouldn't be so happy to know it was Madoka who was playing with his luck just because she finds him cute that way.
Spoiler for Suddenly, IDEAS!:
"For once, 'Megami-sama', could you give this poor existence a break from such misfortunes, and at least bless me a few yen or something? I already got enough misfortune from having my debit card wrecked by a motorcycle from saving that friend to the blue-haired friend of yours, so a few notes wouldn't hurt would it!!??"
"Ahaha, poor Kamijou-san. I'm sorry for playing with you like so, but you're cuter like that. I guess I really should give you something in return, sorry for causing you so much troubles." (Might be a little bit out of character, but screw it, it's the Rule of Funny.)
*A 5000 yen note floats in the air as it slowly falls towards Touma*
*A bird swiftly snatches it away before it gets within Touma's reach*
"... Such misfortune," Kamijou murmured.
"Ahaha... I guess Index-san was right, your right hand won't even let me bless you anything..."
"Enough! Don't say that anymore!! This Kamijou-san is crying knowing his life of misfortunes!!!"
... I really should write that in the fanfiction thread...