Shield Cells are going to have a 5-second delay between pressing the button and getting the recharge. This will definitely make them harder to use, but not solve the problem entirely for me. I think they'll do enough to stop their excessive use in PvE such as we are discussing here, but CMDR's in big ships will still spam them mercilessly. I reckon they should be one per ship and 1-use with a long cooldown or need to be replenished from SYS power. This will bring back more of the combat style of Public Beta and Beta1 with was much more enjoyable IMO, while still extending combat and giving traders that extra bit of survivability. It wouln't hurt to beef up shields generally, as well.
This will obviously make life harder for people like the OP, but an Elite Anaconda should be a very dangerous opponent for a single small fighter. It sould also pay about 10x as much to make it worthwhile for wings (when we get them!) and supermen to pursue as a career. This obviously means that smaller, easier assassination missions and bounties should be available for less powerful opponents.
Advice to the OP? As has been said, make that Viper lighter, for a start. Ditch any gear you don't need that weighs something, like the repair module and never use 'B' grade gear as it is too heavy. If you can't afford 'A' then use 'D'. If you are using all fixed weapons then downgrade your sensors to 'D'. If you only have gimballed MC's then you could probably still stick with D's. Ditch the armour! Viper has strong shields, rely on them. If you are in a Cobra, never go after a fight with fuel tanks more then 50% full; 16t is just ballast. If you are specialising in assassinations then ditch theD3 or A2 for more weight savings. Use chaff abundantly, it will drastically reduce the effect of the Anaconda's weapons. Good luck.