Hi!
側 is read がわ in this context, and it means "standpoint", "side", "party", etc., all of which amounts to "person(s) involved" in the action described just before the 側.
検察側の証人 can be translated as (witnesses concerned with the prosecution).
検察の証人 is translated to (prosecution witnesses).
As for being pronounced (そば), it's when you refer to a position of a place.
Example: 喫茶店のそばに本屋がある。--> There is a bookstore near the coffee shop.
For (がわ), you mainly use it as stated previously or with directions like:
右側 "right side" 左側 "left side"
Hope this helps.