You will get two possible answers, each valid within different regions. If you take ##\sqrt{\sec^2 x} = \sec x## your integrand is ##\tan x##, and is valid in any region where ##\cos x > 0.##. If you take ##\sqrt{\sec^2 x} = -\sec x## your integrand is ##-\tan x##, and is valid wherever ##\cos x < 0.##
If you were doing a definite integral of the form
$$\int_a^b \sin x \sqrt{\sec^2 x} \, dx,$$
you would need to be extra careful about which of these cases to use. If the integration limits ##a## and ##b## happened to be in different regions (that is, in regions where ##\cos x## changes sign) you would need to worry even more about whether the integral even exists at all, since you would be integrating through a point where the integrand is singular. In such a case an ordinary integral might not exist, but a "principal value" integral might---I am not sure.
Note added in edit: I am now sure a principal-value integral does not exist.