May I respectfully suggest the following : Every other reference to leaven in scripture has a bad connotation. You have already pointed out "Beware of the leaven of the pharisees" (also of the sadducees; also of Herod). In the Old Testament the first mention of leaven is that Lot (and despite everything, the New Testament refers to him as a righteous man) baked UN-leavened bread for the angels who visited him and warned him prior to the destruction of Sodom. On the day of the passover the lamb was to be eaten with bitter herbs and UN-leavened bread, and the subsequent celebration of the passover was to be characterised by "no leaven in all your houses". When Paul says "a little leaven leaveneth the whole lump" he was clearly warning against an evil influence (and may have been deliberately borrowing terminology from Christ in this parable). Seems to me difficult to set aside this uniform testimony of scripture in the case of this parable.
Second, note that the idea of "hiding" the leaven in the measures of meal suggests a degree of subterfuge and under-handedness. Then, (I know this will meet with some objections) bearing in mind that the woman is forbidden in scripture from teaching or exercising rule in the church, the fact that this leavening was done by "a woman" may stand for irregularity of procedure.
So the idea seems to be this : There will always be a drift towards the exercise of irregular authority and underhand effort (by whom? - by Satan) intended to infiltrate and pollute the true soul-saving gospel of Christ (thereby making it a NON-gospel, and ineffective for the rescue of guilty sinners) "until the whole is leavened" - i.e. polluted, neutralised and rendered useless and unacceptable to God. Of course the sovereign power of God will never permit things to come to this position. But the means by which He will prevent it is by just the sort of warning implicit in this parable, which puts believers on their guard against teachers who will seek as "grievous wolves" to "enter in among you, not sparing the flock..." This is in line with Jude's clarion call to "earnestly contend for the faith which was once delivered to the saints."
This interpretation of the parable of the leaven seems in line with the preceding three parables of Christ, all of which demonstrate a similarity of thought - that the progress of the gospel will NOT go un-challenged. Parable of the Sower : A harvest only succeeds in 1 out of 4 soil types; Parable of the Wheat and Tares : Satan deliberately sows "the children of the wicked one" among them to create opposition/subversion etc. Parable of the mustard seed (also often disputed) : Growth of the mustard seed into a great tree is unnatural (indeed grotesque) growth, and seems to indicate that the original simplicity which was in the Lord Jesus Christ has suddenly been hi-jacked to become something it was never intended to be - namely a great, outwardly impressive, monolithic structure (you can think of the establishment of Christianity as "official" "proper" and "professional" religion under Constantine, subsequent development of Roman Catholicism, Eastern Orthodoxy, Episcopalianism, Connectional denominationalism etc. - these bear very little resemblance to the true nature of Christianity characterised by our Lord in the Beatitudes ("Blessed are the poor in spirit..." etc.)) Note that "The birds of the air come and lodge in the branches" - again, as recently as the parable of the sower, the birds of the air have the negative connotation of "the wicked one" who "catches away that which was sown..." so the nesting of "the birds of the air" - Satan and his forces - in the topmost branches of the unnatural overgrowth of ecclesiastical structures, is not just something that we see in the unscriptural practises of some organisations calling themselves churches, it is also something which the Saviour anticipated and warned us about.
So the gospel application is this : Do not be diverted into accepting every modern idea which claims to be Christian. Recognise that much of what masquerades as Christian is actually opposed to the true Christ who is revealed in the Bible. Salvation - rescue from sin (not just the consequences of sin) - and eternal life are to be found in Jesus Christ and His work of atonement on the cross. Salvation cannot be found anywhere else. There are many people and ideas seeking to influence the church today to modify this straightforward gospel message and take on board other things as being equally important. But they are like cuckoo's eggs. There is never room in the nest of the true church for Christ's gospel and something else tagged onto it. If allowed to stay, the "something else" will sooner or later push the gospel out. It has happened many times down through the history of the Christian church. Of course we are not required to live in a state of constant suspicion - that would not be Christlike - but neither are we to be naive. There is a constant need for vigilance, lest our churches and gospel preaching should be neutralised by compromise with the creeping pollution of ideas and philosophies antagonistic to the absolute authority of Christ and the holy scriptures.