Your core assumption needs some modification. While there was initially plenty of antagonism between the Bolsheviks and much of the intelligentsia, this did not gut Russian/Soviet sciences as you assume. Instead, in relatively short order, a working relationship was established between the new government and the scientific establishment. Far from being driven into exile en masse, I'd argue that the scientific intelligentsia was the one elite group to emerge from revolution with its position intact.

So let's quickly sketch how this relationship evolved, particularly with regard the 'hard' sciences.

Teachers, professors and employees of the Ministry of Education greeted the 1917 Revolution with condemnations, strikes and a passive withdrawal of cooperation. During the Civil War entire faculties sometimes physically decamped to join the Whites. Not a positive start. This was partly a product of class hostility to Bolshevism - both the student and professor body being relatively privileged pre-revolution - and partly another round in the long-running struggle for university autonomy from the state.

There was significantly less hostility from the Bolshevik side. While some Bolshevik factions (eg Left Communists and Proletkult) ensured that the rhetoric was often shrill, the key figures (Lenin, Lunacharsky and Bukharin) were fairly conciliatory. This was due to both their own intellectual backgrounds, a growing awareness as to the need for technical specialists and a general Marxist appreciation for scientific progress.

(Where the Bolsheviks did of course take a particular interest was in the teaching of social sciences. It was from these that the victims of the 'Philosophers' Ships' were more likely to be drawn.)

Formal rapprochement between the two sides was hesitant during the civil war. The material deprivations bit as hard on the intelligentsia as any other group. And the new Soviet Commissariat for Education (Narkompros) was as chaotic as any of the other new Soviet bodies. It wasn't until 1921 that a charter was in place that formally governed the relationship between state and universities.

But the first steps towards reconciliation had started long before then. Cautious negotiations in 1918 saw cooperation restored with the Academy of Sciences. The latter needed funds and the Bolsheviks were keen to harness its members' technical knowledge. By 1920 Academy scientists were participating directly in state economic institutions (ie VSNKh) and a range of joint research institutions had been set up.

The Bolsheviks, and Lenin in particular, were enthusiastic about the 'hard' sciences but this attitude carried over to higher education in general. From 1919 onwards academics were provided with more rations and higher wages, monetary incentives were restored, old privileges reconfirmed and plenty of Soviet changes (eg the abolition of tenure) were honoured more on paper than reality. Similarly, natural scientists were little affected by censorship and senior academics had direct access to top Bolsheviks. When Pavolv wrote in 1919 requesting permission to emigrate, Lenin himself instructed that he be provided with the funds and equipment needed to continue his studies in Russia.

This continued during the 1920s as, following their technocratic bent, the Bolsheviks were happy to sponsor the expansion of Russian scientific establishments. New universities were established and the growing network of dedicated/professional research institutes allowed academics to retreat into their studies. The Civil War took its toll but overall the Russian scientific community emerged not just intact but, in 'hard' sciences at least, enlarged from its cooperation with the Soviet state.

In short: both Bolsheviks and the intelligentsia had a common interest in developing/funding research. By and large they were able to reach an accommodation that allowed scientists a degree of independence and funding that was acceptable to both. It just took some time to get there.

Sources:

Fitzpatrick's Education and Social Mobility in the Soviet Union spends a chapter looking at the relationship with the professors. It's also a seminal work in examining education in the early USSR in general.

There's also a couple of good essays by Bailes and McClelland that deal with the same topic in Party, State and Society in the Russian Civil War.