Well there is not much you can do about bad start locations, except get tough or start over.
The scientist as a worker, is mostly used to get the one beaker for research from a city that has noting going on or as a 0% research tactic and still get your 40 turn discovery.
Republic is a preferred form to choose for non religious civs. This allows them to get into a good all around government and only make one switch. It should have enough boost to offset the cost of your troops, if you have a reasonable amount of troops and a decent empire. It won't pay for massive armies and non productive cities. If you have mined all the bonus grasslands and even the non bonus ones in cities that do not need more food, you should be fine. With a few rivers and all worked tiles roaded, it ought to be making some money, if research and lux slider is not maxed out.