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I dare!
You're asking grammar/word application of infinitive and present participle, but missed the point that evey writing is a transmission of meaning, not just structure.
She woke up sensing that the ship had stopped.
structurally speaking means while she is sensing (or during the sensing) the ship has stopeed, then she woke up. Thus you equal this meaning as "She woke up because she sensed that the ship had stopped." But the problem of this structural meaning is that the "sensing" action preceed waking up, thus she is sensing during sleeping, which is logically/generally illogical with repect to the human sensation. Unless you want to emphesis her "special ability", this sentence is "strange".
She woke up to sense that the ship had stopped.
structural speaking can mean as you said She woke up and sensed that the ship had stopped. But the problem in writing "to sense" means an active action, but sense is a "passive" meaning word, thus the senstence's actual implied meaning is that She woke up with the intention to "detect" that the ship had stopped. which mean the reason she woke up for the purpose to sense whether the ship is moving or not and found that it had stopped.
So my dare conslusion is that both sentence is "wrong" in describing the actual situation with a reasonable logical and normal behaviural meaning.
In fact, the sentence that is both logically in meaning and grammatically correct is:
She woke up and sensed that the ship had stopped.
And for the 2nd meaning that while she's sleeping she sensed the ship had stopped then she woke up:
She woke up with a sense that the ship had stopped.
參考: Anaswer from someone with no English Certificate. And English Degree must be able to answer much better to your satisfaction.