Is learning kanji with furigana in japanese helpful or not?

Well, it's better than learning with pure hiragana. At least you're seeing the kanji. You also have the option of covering up the furigana with a piece of paper or something and revealing them only if you need to.

Also, if your kanji knowledge is limited it can be incredibly time-consuming and frustrating to look up every other word. If you don't know the word, having the furigana there is a big help for looking up words.

The downside obviously is that you might end up ignoring the kanji and just reading the hiragana, which won't do much to improve your kanji reading skills.

Well, I think so. There are multiple readings for Kanji in Japanese, such as On'yomi (which is derived from the Chinese Language), and Kun'yomi (which is the native reading). Thus, Furigana is useful if you want to read the Kanji correctly as it is Hiragana that is written on top or at the side of the Kanji, and thus aids you in reading Kanji if you have a knowledge of Hiragana.