What guidelines are helpful regarding the use of Baptismal water in light of any events (past, present, future) involving the spread of diseases?
The Book of Blessings, no. 1085, provides the most comprehensive description of a baptismal font:
The baptismal font, particularly one in a baptistery, should be stationary, gracefully constructed out of suitable material, of splendid beauty and spotless cleanliness; it should permit baptism by immersion, whenever this is the usage (cf. Christian Initiation, General Introduction, no. 25). In order to enhance its force as a sign, the font should be designed in such a way that it functions as a fountain of running water; where the climate requires, provision should be made for heating the water (cf. ibid., no. 20).
How this "spotless cleanliness" of the water is maintained is an interesting question. The use of filtration or even "ultra violet" systems of purification are helpful, but are ultimately of limited value. Standing water will, even after a short period of time, serve as a fertile medium for various pathogens. This is especially true when we follow the Church's recommendation: "If the consecration of water has taken place at the Easter Vigil, the blessed water should, insofar as possible, be kept and used throughout Easter Time to signify more clearly the relationship between the Sacrament and the Paschal Mystery." (Christian Initiation, General Introduction Number 21).
This issue is similar to those surrounding health concerns with the exchange of a sign of peace or the sharing of the common cup at Mass. Our interaction with persons or groups of persons in society or in the liturgical assembly is always attended by varying degrees of the risk of disease. The issue addressed is a question of balancing the avoidance of disease and the value of certain liturgical practices. The most one can expect is that reasonable efforts be expended to reduce whatever risk may be involved, to whatever extent that this is possible.