It's not penny pinching over security costs. The primary reason is that the extra time taken for the stop and impact that has on the capacity of the line means if Eurostar stopped at Stratford you wouldn't be able to run as many trains in a day. The extra time for the Stratford stop is something like 7 minutes for an E300/Cl.373, which makes a difference when you're competing on centre-to-centre times against an aeroplane. Somebody with access to the SRTs will need to let us know what the penalty is for an E320/Cl.374.The rail journey takes 7 mins, but you have to build in waiting time, transit time on lifts escalators and a back up plan in case of delays etc all with luggage and if catching an early Eurostar it certainly has just put me off using it to Rotterdam, as it is if I am connecting I may as well just go to city airport and have a quicker journey time.
A lot of travellers will be using it for business, there are huge numbers of businesses relocating to Stratford now, it seems senseless to have built a station costing billions only to penny pinch over over relatively small security costs. You would have thought the landlords at the Olympic Park would have been asked to / or offered to pay to support it given the increase in attractiveness it could provide for the site.
There is an element of cost to it, in that if you stop any international train at any of the 3 intermediate stations, you need to stop a minimum number of trains to justify the operating costs of the security and border force requirements. This minimum viable number of trains then exacerbates the capacity problems outlined above.