You create rampless channels to get the light coming through the surface, and then you let the light in deeper and make a roof by building walls on the level below the surface. Constructed walls create a floor on the level above them, and this seals off your growing area without your dwarves having to stand topside to put floors down directly. For this to work properly, there needs to be no physical access to the surface during periods when the surface is being channelled.
Here's the completed setup for a 3x3 farming area, with the access being on the right:
, = soil floor
+ = wall top
O = constructed wall
# = natural wall
>, <, X = stairs
_ = channel here
z+0
,,,,,,
,+++,,
,+++,,
,+++,,
,,,,,,
z-1
######
#OOO>#
#OOO>#
#OOO>#
######
z-2
######
#,,,<#
#,,,<#
#,,,<#
######
It starts out like this:
z+0
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
z-1
######
#XXX>#
#XXX>#
#XXX>#
######
z-2
######
#<<<<#
#<<<<#
#<<<<#
######
The next part is rather fiddly and needs to be done in sequence, so you may wish to burrow your miners for a quicker response time. You'll need to include the surface level in the burrow, though they'll never actually be on it. Another option is to channel out all of z-1 and then construct stairs, deconstructing them in sequence instead of mining them in sequence.
Step 1:
z+0
,,,,,,
,_,,,,
,_,,,,
,_,,,,
,,,,,,
This digs a row of channels in the surface, letting the light through into z-1. No ramps are created, because the level below the channel is already dug into stairs.
Step 2:
z-1
######
#_XX>#
#_XX>#
#_XX>#
######
This lets the light through into z-2.
Step 3:
z-1
######
#OXX>#
#OXX>#
#OXX>#
######
Build walls, using the areas you're going to dig out next as scaffolding.
Step 4: Repeat Steps 1-3, moving in rows from left to right.
You can channel all of z+0 at once if you're comfortable with opening up that large a gap, but the up/down stairs beneath them have to be removed one row at a time. Once all tiles are Inside, you can either remove the stairs on z-2 and start using the farm, or dig a shaft as deep as you like. Natural stairs block light, so at some point you'll have to make everything between the final farm area and the roof Open Space.
You can also use the up stair + channel method to dig moats from beneath, which may be useful in acquiring plants for the farms. Those islands will be vulnerable to fliers though.
Deadly rain will remain something of a problem. There's a short window in which a dwarf can be standing on a tile that's open to the air.