Honestly, I don't think the Latin change in this regard was motivated by hygenic concerns, or worry over illness.
Like every minimalization the Latins employed after the schism, it was employed at first for practical reasons, and then kept in place just to "prove" something to those who had problems with it.
Case in point...
It is almost certain that the Latins began the practice of communicating their congregations "under one species" (the Host) for purely practical reasons. While I'd have hoped they'd have taken a que from the East, and simply introduced the use of the spoon (which makes concerns about spillage, or people palming the Holy Gifts just as irrelevent, without depriving them of the basic form of Communion which it is obvious Christ desired His followers to receive at the Eucharist), this was their "pragmatic" solution, which in turn they could justify on the grounds of "concommittance" (the teaching that, strictly speaking, because Christ is Risen, one cannot receive only His Body when receiving the Host, or only His Precious Blood when drinking from the Chalice; rather, since He is alive and living, one, by connection, receives both in each "species.").
And when the inevitable occured (some complained on the grounds of apostolic tradition), the Latins became more dogged - now rather than simply existing for practicality's sake (and perhaps, in the popular consciousness, to re-inforce clericalism...since the priests certainly did receive "both kinds"), the practice (oddly enough) stood to "resist the heretics" (those who denied, explicitly or implicitly, "concommitance".)
It was long similar with Baptism - I suppose it's "easier" and on the whole less difficult, to pour a little water over someone's head, then dunk them whole and entire into a baptismal pool. In a minimalistic mentality, the only question was "is this valid?" And since the Latins answered "yes" to this, they went ahead and did it. Then, round aboutly, when some people complained (on the grounds of tradition and apostolic practice), they became more stubborn in the practice, simply to confound these dissenters.
I think it is a terrible thing, when Divine Services in general (not just Baptism in particular) are treated in such a calculating way. Is this the Spirit of the New Testament? "Do the least we can possibly get away with, just enough so that we can get through the door"?
The problem with such a mentality, is that in our fallen state, the minimalist attitude itself (and not necessarily all of it's particular manifestations) will doom us to self satisfaction, even a "bargaining" mentality towards God, in which we figure "I jumped through the necessary hoops; it's all good." This is totally alien to the mind of the Fathers - and I include those of the west, first and foremost.
Don't get me wrong - such questions are not totally without value. However, when they become the way pastoral/liturgical decisions get made, I fear it is poisonous, as it will, one way or another, affect not only people's attitudes within the Temple, but outside of it as well.
Thus, even though the Didache says that if necessary, baptism by infusion is permissable, it certainly does not portray this as the ideal. And why? Because while it certainly fulfills some kind of "minimal" symbolism needed to "show" in figure the invisible grace of the Mystery, it leaves out so much. While baptizing someone with a little water on the head does minimalistically symbolize "washing" and reflects baptism's Trinitarian aspect, does it reflect buriel in Christ, and Ressurection? Does it even fully demonstrate the total cleansing of the soul which Baptism affords, the way immersing somone in a font (or natural body of water) does?
This "calculating" (it's the best term I can think of) attitude is infectious. This is part of the reason why in Catholicism the economy of salvation began to be treated solely in a judicial/legal context; even penance was reduced to this (with indulgences serving as a way to avoid them, or at least mitigate them - based on the understanding that the primary purpose of penance is not reform and real, objective change in the soul...but rather the "paying up" of something you owe to God, which strictly speaking can be done by someone else if He's willing to accept that.)
I'm not saying that the particular practice of "baptism by pouring" as a policy is responsible for all of this; only that it is a manifestation of a fundamentally flawed way of thinking.