Imho, there are two aspects to this...
Opposition to eastern religious philosophy had been very high in western society and the likes of Vivekananda and Yogananda and others were subjected to false slander and propaganda. This was also the same for Buddhist religious philosophies as well. Even christian leaders who propagated interfaith dialogue or assimilated eastern teachings were subjected to opposition, and the untimely deaths of Anthony de Mello and Thomas Merton had lead to a couple of conspiracy theories as well.
Creating a couple of false witnesses and fabricated evidences to disparage a popular leader is not a big deal in today's world, and such tactics are used in other issues as well.
So a propaganda campaign should not be ruled out as a cause for this controversy.
Secondly, it is possible that Vishwananda had indeed engaged in improper conduct. This can be because he has not gone through the necessary austerities to ensure proper self-awareness and self-regulation at all times.
He seems to be a bhakta yogi, and practice of Yoga can result in opening of Kundalini and high sexual energies. Such sexual energies can be trasmuted to higher states of consciousness if the yogi is well-trained and disiciplined and have a good personal regimen of daily sadhana and exercise.
If such traits are lacking, the tremondous force of Kundalini can result in masturbation or high sexual activity which can cross limits even if the aspirant is well-intentioned earlier.
As an Indian saying goes, it is only a well-baked pot that can hold water.
This also holds true for all other religions as well. We regularly hear of criminal acts of a sexual nature in Christian monks and Islamic preachers and others too, mainly because they were not able to handle the surge in Kundalini that comes with prayer and devotion even though they were essentially good people with noble intentions. Lack of knowledge of the kundalini process is an important factor.
Swami Vivekananda had himself stated of this phenomenon...
‘During meditation, suppress the emotional side altogether. That (emotionalism) is a great source of danger. Those that are very emotional, have no doubt their Kundâlini rushing quickly upwards, but it is as quick to come down as to go up. And when it comes down, it leaves the devotee in a state of utter ruin. It is for this reason that Kirtanâ and other auxiliaries to emotional development have a great drawback. It is true that by dancing and jumping etc., though a momentary impulse, that power is made to course upwards, but it is never enduring. On the contrary, when it traces back its course, it rouses violent lust in the individual.
Listening to my lectures in America, through temporary excitement many among the audience used to get into an ecstatic state, and some would even become motionless like statues. But on inquiry I afterwards found that many of them had an excess of the carnal instinct immediately after that state.’ ~ Swami Vivekananda
When Swami Vivekananda was giving lectures in America it appears that some people in the audience started shouting, 'Hail Jesus, Hail Jesus,' and 'Glory to the Lord.' Here the kundalini was raised because they were all bhaktas [followers on the path of devotion] but as soon as they went home it appears the kundalini went lower than normal.
Swami Vivekananda says that they were emotionally awakened without any yama and niyama [disciplines and observances of spiritual practice], without any purity, and therefore they turned out to be brutes. And when you become brutish then by sheer will you have to give up all those things that you want to do in a sensual way. It is that easy. Do not go to a guru to correct it, you can correct it yourself. How? Try to do away with all those sensual things and do more japa [meditative repetition of a mantra or one of the many names attributed to God]. ~ Mother Radha
So an inability to deal with rising Kundalini due to inadequate practice could be a reason for possible immoral conduct on the part of Vishwananda.
Vishwananda looks young and unseasoned, and in the company of devotees who insisted on taking care of his needs probably had an easy life instead of a spartan and simple life a monk is supposed to lead. It is possible that he may have been overconfident, shirked his daily regimen of duties and exercises, and consequently was not able to deal with properly managing his kundalini flow resulting in issues later on.