Learn French: Si, notre allié est très pacifique.

In French, si is the specific word used to say "yes" when you are contradicting a negative question or a negative statement. If someone said, "Your ally is not peaceful," or asked, "Isn't your ally peaceful?", you must use si to correct them and say, "Yes, he is!" If the original question had been positive, you would just use oui.

Is allié related to a verb, since it looks like a past participle?

Yes! The noun allié comes directly from the past participle of the verb allier (to unite or to ally). It is very common in French to use past participles as nouns. If the ally were female, it would be spelled alliée, but pronounced exactly the same.

If the ally were female (notre alliée), would the word pacifique change?

No, it wouldn't change. Most French adjectives add an -e to become feminine, but because pacifique already ends in an unaccented -e in its masculine form, it stays exactly the same when describing a feminine noun.

I always mix up notre and nos. Why is it notre in this sentence?

You use notre because the following noun is singular: there is only one ally (allié). It means "our (single) ally". If you were talking about multiple allies, you would use the plural form nos, making it nos alliés (our allies).