TN prof says some species of eucalyptus has been reported to be toxic to fish, but species that aren't commercially available.
http://plantsciences.utk.edu/pdf/PlantsthatPoisonFish.pdf

Certain native Australian eucalyptus have been reported hazardous to fish.
http://www.ecofilms.com.au/toxic-plants-around-your-aquaponics-system/

Gehrke et al. (1993) showed that accumulated litter under river red gums, Eucalyptus camaldulensis, in the Murray Darling Basin produces polyphenols associated with 'blackwater' when inundated, and these compounds are highly toxic to fish if the water is not well flushed.

Gehrke P., Revell M.B. and Philby A.W. (1993). Effects of River Red Gum, Eucalyptus camaldulensis, litter on golden perch, Macquaria ambigua. Journal of Fish Biology 43, 265-279.

Eucalyptus spp. contain high levels of phenolics and terpenoids which can be toxic. Animals such as the koala which eat Eucalyptus have developed methods for detoxifying the compounds in the liver. In addition, they have bacteria that degrade tannin-protein complexes. Most animals do not have this ability.
http://www.ansci.cornell.edu/plants/medicinal/eucalyp.html

Dissolved organic carbon (DOC) can induce lethal and sub-lethal effects in exposed biota via hypoxic blackwater events and the toxicity of leached compounds.
MORRONGIELLO, J. R., BOND, N. R., CROOK, D. A. and WONG, B. B. M. (2011), Eucalyptus leachate inhibits reproduction in a freshwater fish. Freshwater Biology, 56: 1736–1745. doi: 10.1111/j.1365-2427.2011.02605.x

So I think the answer is some eucalytus may be harmful to fish under the right conditions. From quick read of some of the above, getting the leaves out or decomposed would not hurt. Flushing and keeping high DO levels also sounds beneficial.