It depends on the dating of the individual changes. It's known that short -i and -u (including -u from earlier -ō) were lost after heavy syllables in West Germanic, but kept after light syllables (Old English still preserves this). However, the ending of ja-stems is always -i, no matter what; it's never lost. So that means that it can't have been -i at the time that ending was lost, but must have been -ī. At some point in Frankish history, unstressed long vowels started to be shortened, but we can't know when that happened, nor do we know for sure when -i and -u were lost after heavy syllables. However, the shortening must have happened after -i was lost, otherwise it would have been shortened and then lost too. I don't know if -i and -u were already gone in Frankish, or whether they were preserved and only disappeared later on. The fact that they were lost in the same way in all West Germanic languages suggests that they were lost early, but the ja-stem ending was probably still -ī at that time.
You make a convincing argument ;-). It would probably be good if we move this discussion to some major talk page, so others will know where to cite our decisions.