It is true that The Pyramids are central to obsolete's wonder based economy where he relies on the beakers from Representation and settled specialists to do a lot of his research. But he is not running a SE, since he he has few if any food specialists. I think the original poster is asking what to do with a conventional SE if he fails to win the race for The Pyramids.
As many have already said, I consider The Pyramids to be unecessary for a SE. In fact on many maps it is easy to argue that HR is superior to Representation anyway, providing more happiness and giving much better flexibilty in controlling it. It depends on your gameplan but SE is particularly suited to warfare. There are too few specialists to make early use of Representation worthwhile in the same way it is in the middle and late game. That means it is feasible to research Constitution normally (using some lightbulbs towards Liberalism and taking Nationalism) in a SE and out research a slower CE based economy. That makes The Pyramids an expensive (500 hammer) distraction from REXing or an Axe rush.
But working a scientist for 34 turns gets you one great scientist, which can be used to bulb a tech (worth 600 to 1200 beakers), and the other uses can be more powerful than that over the long term! So the scientist is worth it to get your first great person, even if we ignore the 127.5 (3*34*1.25) beakers he gives you.
I would say that you should only lightbulb techs that use all of the 1500 + 3*pop beakers a GS is worth. Anything less is wasteful. That normally means Education and higher techs, depending of difficulty level. An exception I make to this rule is lightbulbing Philosophy (circa 1290 beakers on Monarch IIRC), if I want to found a religion (needed for Pacificism) and enabling an early switch to Caste System and Philosophy together. That early switch recovers the beakers "lost" and helps with the race to Liberalism. I think a GS at this stage of the game should be considered as being worth 1500 beakers as a minimum and is typically 1600. So the first 4 GS are worth something like 6000 beakers in total and are usually enough to win the Liberalism race (use say 1 GS for an Academy, 1 settled and 2 lightbulbed)
In the same way we look at the growth and development of cottages we can study the build up of GPPs in a city's GPP pool. The first 4 GPs only costs a total of 1000 GPPs. If generated entirely by running 2 scientists in a library, usually in several cities in parallel, this takes a total of 334 scientist-turns each giving 3 GPPs. This is even easier for a Philosophical leader who gets 6 GPPs per scientist per turn. Running Pacificism gives another 3 GPPs, and is especially useful for a Spiritual leader.
Generating the 1000 GPPs costs 668 food (for non Philosophical and without Pacifism) and they are worth a total of 6000 beakers (see above) so we can argue that each GPP is worth 6 beakers and each food is therefore giving 9 beakers

That means a humble grassland farm, providing 1 food per turn, is giving 9 beakers (from GPPs) plus half of the 3.75 beakers a scientist gives, totalling 10.87 beakers per turn per farm. That is massively more than any cottage could give at that time and accounts for why a SE is so powerful in the early game. But note; if Representation was added it would only give another 1.87 beakers to this total and this is why it is a distraction at this point in the game. Building The Pyramids delays REXing (probably by several 10s of turns) and that delays running the scientists needed to produce the 1000 GPPs. Obviously running a lot of scientists each giving 3.75 beakers and 3 GPPs is better than running a few (or none) giving 7.5 beakers and 3 GPPs when each GPP is worth 6 beakers.
Getting to Constitution is a magical thing for a SE. It not only allows Representation to be run but also allows Jails to be whipped into key cities. Now the SE economy can move into a mixture of research and espionage which supports a domination push perfectly. Adopting Nationalism is a perfect fit and allows 25% more EPs, +2 happiness and Drafting (once you have researched something worth drafting

).
Is it even worthwhile to try to run an early game SE without the Pyramids (ie. Representation)? Or is it best to just try a CE? Also, how likely is it to miss the Pyramids if you beeline to it w/o stone and w/o industrious on Emperor, Immortal, and Diety?
I mean it seems like if you can't get representation, it's not that good because basically you are getting 1.5 beakers/gold a tile (it takes 2 farms to support one specialist), whereas a cottage is 1 commerce a tile. After 10 turns, a hamlet produces 2 commerce, with only more room to grow and outpace the SE.
A SE still has GP's, but can they really compensate for a non-representative SE's weaknesses?
So what do you do if you failed to get The Pyramids? Give a sigh of relief

and get on with playing an aggressive SE. HR will be perfectly good enough for an early war or two while you research towards Constitution.
I hope I have shown with the maths above that the main research output at this time in the game can come from GPPs. GPPs provide beakers far more efficiently than cottages or Representation can. In fact Representation is often a distraction and weaker than HR in the early game. With this method as others have said cottaging the capital can be especially worthwhile and sets up a perfect Science City for building Oxford that can continue to research strongly afterwards when it is harder to make GPs due to their increasing costs. Alternatively, you can switch the emphasis of your SE from pure research to a mix of research and espionage.
EDIT: It seems Futurehermit replied while I typed out this long post

I hope I have provided some mathematical back up for the points he makes.