They are still there in the old prayer books that will still be used by parishes. However, the Studite Fathers in Ukraine have issued a revamped series of liturgical prayers to St Josaphat that does not have those phrases.
They do a great job of republishing the old liturgical services but leave out the more Latin feasts and 'angry' notes such as you have indicated.
Orthodox have no problem purchasing their liturgical and other spiritual books for their own use as a result. This same principle is followed by the "Russicum" in Rome or the Russian Catholic College who publish liturgical material that Orthodox can use as well.
The more "pro-Latin" elements in the Eastern Catholic Churches have tended to turn St Josaphat into something he was not in life - an "Orthodox basher."
Josaphat was very careful never to offend Orthodox sensibilities with respect to liturgical and monastic traditions (e.g. he strenuously resisted the introduction of the Carmelites into the East, saying this would be seen as an overt Latinization - however, the Carmelites WERE in fact an Eastern Order that became Westernized after they left the Holy Land).
Josaphat observed, to the minutest detail, the Eastern rules and the typikon of St Basil the Great (he once corrected Orthodox monastics who were about to go hunting and asked them where in the Asketikon of St Basil did the Holy Father allow monks to hunt . . .).
When Josaphat lay in state after his death for several days, Orthodox came to observe his body. Perceiving that it wasn't corrupting, a number of them actually acknowledged him a saint right there and then, and kissed his hand (some of these became Catholic, others didn't).
The Orthodox, we should remember, have their own Martyr - Saint Athanasius, Archimandrite of Brest.
Athanasius didn't like the fact that secular powers were imposing the Union of Brest on Orthodox parishes. For his outspokenness, he was made an example of and was tortured for several days by Catholics. He was then taken to a forest by gendarmes and there had to dig his own grave before being shot twice and then buried alive.
Eastern Catholics, in fact, venerated St Athanasius very highly for having stood up to their oppressors at the time. St Athanasius' feast day is Sept. 18th and the Jesuits, to try and dissuade this cult, placed the feast of St Josaphat on Sept. 16th (the idea that people wouldn't want to celebrate church festivals so closely together and would therefore focus on St Josaphat rather than on St Athanasius). The plan didn't work, but Metropolitan Andrew Sheptytsky of Lviv and Galicia later ordered St Josaphat's feastday to be returned to its original day, November 12th (November 25th on the true . . .er, I mean JU-lian calendar
I will try and locate the troparion and kontakion expunged of its anti-Orthodox content for you.
It is best to commemorate St Josaphat via the general Service to an Hieromartyr.