At least in autopair, if you press "C-q (", it will insert a literal
"(" without autoclosing. I don't know about paredit. You can also use
a primary field transformation to allow you to choose the string to
insert (and thus choose only between the parenthesis you're interested
in). To do this look at the (quite outdated, but should work)
documentation.
Other that that, disabling a minor mode while a snippet is active
(notice that this is different from snippet expansion time), can only
be done, but not very cleanly, with `yas-exit-snippet-hook`, which to
make matters worse, is not snippet specific, so you would have to set
a variable in the snippet's body and restore it in the snippet hook.
One can't use normal lispy methods of wrapping a command call in a
dynamic environment because typing into a snippet is done in multiple
commands.
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João Távora