The Ukrainian hostility is enough reason to detour its entire airspace. That might be the safest option for all Russian flights, or there will be more cases similar to MH17 otherwise.
Suspension of flights to those destinations is an expected economic extension of the political dispute between Ukraine and Russia.
It is very unfortunate to see an airport shutting down like that.
It is quite strange to start talking about infrastructure limitations after only 4 years of operations. Terminal D of Sheremetyevo was inaugurated in 2009 exclusively for Aeroflot.