How about poking him with a needle?
If she's so damn sure of herself that she'll jump off a building, to her death if she's wrong, which by the way ceases to leave her in control once she's entered free fall, then trying to puncture Clark with a sterilized needle is by comparison an infinitesimal risk.
First off, where's she going to get a sterilized needle on short notice? Second, if he's Superman, then he's going to sense her coming with the needle and will dodge, or will use a burst of heat vision to break his skin. He's had a lifetime of practice at hiding his invulnerability; a simple trick like that isn't going to be enough to get past his guard.
Third, Lois Lane has never
been one to play it safe. If you don't want her to do things that are "against character," then you're contradicting yourself by proposing this.
Fourth, sometimes being in control of an overall situation entails choosing to surrender that control at certain moments, with the confidence that you've arranged things in such a way that it will turn out all right. Like when you jump out of a plane after carefully checking your parachute. In this case, Superman was Lois's parachute, and she was confident that she'd made the checks correctly. Which, let's remember, she had. This version of Lois Lane figured out that Clark was Superman just by looking beyond the glasses, and that alone makes her smarter and more in control than just about any other Lois Lane.