I would personally read it as いっぺん, but both are used in the hiragana form: いっぺんの雲 (rare) and ひとひらの雲 (less rare). I assume the latter is used more often in hiragana form exactly because the former is what you would normally read it as, hence necessitating the use of hiragana when the intention is to use the latter. ひとひら in this context sounds kind of "poetic" (or "beautified") to me.
For what it's worth, 大辞林 gives the following example for いっぺん：
③ わずかばかり。ほんの少し。 「－の雲」 「－の良心もない」
With this definition it would often be used together with ～もない or a similar expression though, as you can see in the second example. On the other hand, 新明解国語辞典第五版 provides the following definition for ひとひら：
〔雅〕いちまい。 「―の雪」 [表記]「一《枚」とも。
Here, the〔雅〕denotes the following (from here):
"Gago: Wago that do not see much use in relaxed contexts, but that are common in tanka, haiku and other forms of poetry, as well as in texts written in literary style."
which seems to be highly congruent with my initial impression of how this reading would be used in practice.