Well, the idea that she's not powerful enough to take them both is an inference you made, rather than the characters.
By her own assessment of her abilities, she believed she was capable of holding her own and that would have been reckless or foolish if the information given in the book and in others had not supported her assessment. However, it was not only Diana that believed she could pose a major threat to both of them, but Zod as well. Zod was the one who suggested the withdrawal rather than fight Diana even with Faora's help. By Zod's assessment, she was enough of a threat that even a two on one fight was too risky in his mind. This is supported by the fact that neither Zod nor Faora were even able to touch Diana during their brief exchange. Diana's own assessment of her chance against Kryptonians was also supported by the fact that she's done very well against them in new 52 canon. Her only two other battles were against Supergirl and Superman, the former of whom she was able to demolish with minimal effort and the latter of whom she was able to bleed and knock for a loop with a single kick. Her assessment and her threat wasn't made without precedent. She's taken on New 52 Kryptonians before and won.
I'd argue that she came off as more overbearingly confident in Simone's Genocide arc. During her third battle with Genocide, she made a similar, far more over the top threat by asking what direction Genocide would like to face when her head was mounted on a pike. Similarly, it was phrased as an inevitability rather than a threat. The difference was, that unlike with Zod and Faora where she had previously done extremely well against similar opponents and even her opponents believed that she could defeat them, her track record with Genocide suggested that she had no chance to win. In her first fight, she was defeated by Genocide rather easily and beaten viciously to the point of near death. In her second fight, she was destroyed again, even when she had Donna Troy, Wonder Girl, Green Lantern, Firestorm, Black Canary, Red Tornado, Vixen and the Gorilla Knights to back her up. One could argue that making a threat in this situation was infinitely more foolish than taking on two Kryptonians. However, she was able to back up her threat and Zod implied that she could have done just that in this issue.
Essentially, the threat would have been reckless and foolish if there had been no precedent when it came to her battles with New 52 Kryptonians, but she has done extremely well in her battles against them and Zod himself believed she could win.
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